Fishing for Genes in the UCSC Browser
A Tutorial
Rachel Harte <hartera@soe.ucsc.edu>
Mark Diekhans <markd@soe.ucsc.edu>
University of California, Santa Cruz, CA
Version 1.0
September 18, 2008

Abstract
This tutorial is aimed at the biologist who is interested in exploring protein-coding genes
using the University of California Santa Cruz (UCSC) Genome Browser. It is geared towards
those who have little or no experience using the UCSC Genome Browser and for more advanced
users who are not familiar with many of the gene-oriented browser features. Using the example
of a human gene, PPP1R1B, the reader is guided through a step-by-step process for finding
and visualizing protein-coding genes in the context of the human genome and a wide variety ofgenomic data. The user is shown how to use the UCSC Genome Browser to locate a Mammalian
Gene Collection (MGC) clone of the gene and how to order the clone from suppliers.

Fishing for Genes in the UCSC Browser

1

Accessing the UCSC
Genome Browser• Genome Graphs on the side blue bar is atool to facilitate viewing of whole genome
datasets such as genome-wide SNP association studies, linkage studies and homozygosity mapping. Instructions are in the
Genome Graphs User’s Guide• PCR on the top blue bar or In Silico PCR
on the side blue bar is a fast method ofsearching for a pair of PCR primer sequences in a genome assembly.
• VisiGene is a virtual microscope for viewing in situ hybridization images.
• Proteome on the top blue bar and Proteome Browser on the side blue bar leadto the gateway of a tool for viewing proteins and their properties[14]. Both graphical images and links to external websites
provide a rich source of protein information.
• Utilities on the side blue bar allows accessto various tools to remove non-sequencerelated characters from DNA or protein, forcreating a gif image for a phylogenetic tree
and a tool which converts genome coordinates between assemblies (liftOver).
• Downloads on the side blue bar allows
bulk download of data including dumps
from the Genome Browser databases.
• Custom Tracks is a powerful tool allowing users to add their own data for viewing and querying within the context of agenome and its associated annotation data.
A User’s Guide provides help for creating
Custom Tracks.

The UCSC Genome Bioinformatics website
consists of a suite of tools for the viewing andmining of genomic data. The UCSC Genome
Browser [16, 18] facilitates the viewing ofclones from the Mammalian Gene Collection(MGC)[35, 37] in the context of other genome
annotations. Various types of annotations suchas MGC Genes are visualized in tracks which
are graphical representations of data displayed
in a genomic context on the Genome Browser.
To view these annotation tracks, first go to thehome page at http://genome.ucsc.edu (Figure 1).
The blue menu bars at the top and the left sideof the Genome Browser home page both include
following links to various tools (Figure 1):• Genomes on the top blue bar or the
Genome Browser link on the side blue
menu bar allow entry to the Gateway pagefor the Genome Browser. From here, users
may select the genomes that they wish
to browse. An additional route of entry is via a Photo Gateway page in the
UCSC genomewiki with photographs ofeach species whose genome is represented
in the UCSC Genome Browser.
• Blat is a fast alignment tool[20] which allows the user to align DNA or protein sequences to the genome assemblies.
• Tables on the top blue bar or Table
Browser[17] on the side blue bar link to aninterface allowing the retrieval of data associated with tracks from the databases underlying the Genome Browser. Data added
as additional tracks created by the user
(Custom Tracks) may also be queried withthis tool.
• Gene Sorter is a tool that displays a sorted
table of genes that are related by some metric selected by the user e.g. similar expression patterns, protein homology or proximity in the genome[19].

2

Searching for a gene

Let’s suppose that a user wishes to study the human PPP1R1B (protein phosphatase 1, regulatory (inhibitor) subunit 1B) gene, which is expressed in the brain. The protein encoded bythis gene is also known as DARPP32. Its phosphorylation status is regulated by dopaminergic and glutamatergic (NMDA) receptors. Once
1

Fishing for Genes in the UCSC Browser

Genomes - Blat - Tables - Gene Sorter - PCR - VisiGene - Proteome - Session - FAQ - Help
GenomeBrowser
ENCODE

Gateway

About the UCSC Genome Bioinformatics Site
Welcome to the UCSC Genome Browser website. This site contains the reference sequence andworking draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE
project.

Blat
Table
Browser
Gene Sorter
In Silico
PCR
GenomeGraphsWe encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls
over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression,
homology and other information on groups of genes that can be related in many ways. Blat quickly
maps your sequence to the genome. The Table Browser provides convenient access to the underlying
database. VisiGene lets you browse through a large collection of in situ mouse and frog images to
examine expression patterns. Genome Graphs allows you to upload and display genome-wide data
sets.

VisiGene

The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, across-departmental team within the Center for Biomolecular Science and Engineering ( CBSE) at the
University of California Santa Cruz (UCSC). If you have feedback or questions concerning the tools ordata on this website, feel free to contact us on our public mailing list. To view the results of the Genome
Browser users' survey we conducted in May 2007, click here.

Proteome
BrowserNews

GalaxyUtilities
Downloads
Release Log
CustomTracksArchaeal
Genomes
Mirrors
Archives
Training
Credits
Publications
Cite Us
Licenses
Jobs
Staff
Contact Us

To receive announcements of new genome assembly releases, new software features, updates andtraining seminars by email, subscribe to the genome-announce mailing list.
26 June 2008 - New Worm Genome Available
Along with the set of worm browser updates that we're currently releasing, we've added a newnematode to the collection: Caenorhabditis japonica. This genome assembly (UCSC version
caeJap1, Mar. 2008) corresponds to the v. 3.0.2 assembly produced by the Genome Sequencing
Center at the Washington University St. Louis (WUSTL) School of Medicine.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP
server or Downloads page. Please review the WUSTL data use policy for usage restrictions andcitation information.
We'd like to thank WUSTL for providing the sequence data for this assembly. The UCSC caeJap1
browser was produced by Hiram Clawson, Ann Zweig, and Donna Karolchik. See the Genome
Browser Credits page for a detailed list of the organizations and individuals who contributed to thisrelease.
20 June 2008 - Two Worm Updates Released: We've updated our browsers for
the C. remanei and C. brenneri nematode genomes. Read more.
10 June 2008 - Lamprey Browser Released: We have released a Genome
Browser for the Mar. 2007 assembly of the lamprey genome, Petromyzon marinus. Read more.
10 June 2008 - Lancelet Genome Available in Browser: The Mar.
2006 release of the lancelet genome (Branchiostoma floridae) is now available in the UCSC Genome
Browser. Read more.

Figure 1: UCSC Genome Browser home page. On this page, there is an introduction to the web
Feb. assemblies
2008 CavPor3 and
5 training
June 2008- Guinea
Browser
Released:site and postings of news of
seminarsand Pig
recentadditionssuch asThenew
release of the guinea pig genome (Cavia porcellus) is now available in the UCSC Genome Browser.
software features. The blue
menu
bars
at
the
top
and
left
side
of
the
page
allow
access to theRead more.
Genome Browser for genome assemblies of a variety of organisms, data mining tools and help
pages.
2

Fishing for Genes in the UCSC Browser

35046403 link. This will take you to
the PPP1R1B locus in the human genome.
Note that there are two RefSeq splice variants listed for this locus and this one is thelonger transcript variant.

phosphorylated, PPP1R1B, is a potent protein
phosphatase-1 inhibitor. To visualize this genein the UCSC Genome Browser in the context ofvarious genomic annotations, the user may takethe following steps:

1. To get started, clicking on either the
Genomes or Genome Browser link will
3 Genome Browser
take the user to the Gateway page where
annotation tracks
the clade, genome and assembly of interest may be selected from pull-down listsof multiple organisms and genome assem- The Genome Browser displays certain annotation tracks by default in the main Browser imblies.
age. The current default display (Figure 4)
2. Below this area, there is a section describ- shows a number of gene tracks:
ing the selected assembly which also indicates that the default assembly (at the time
• UCSC Gene predictions[15, 18]of writing) is known as hg18 on the UCSC• BLAT alignments of sequences from
Genome Browser website. This assembly is
GenBank[2]also known as NCBI Build 36.1. This sec• BLAT alignments of full-length ORF MGC
tion also contains a list of Sample position
Genes.
queries. These are a selection of queries
that may be entered into the position or
Other visible tracks in this default display are:search term box adjacent to the genome
and assembly controls. Examples include• Vertebrate Conservation[29]gene name, mRNA or EST accession and• Simple Nucleotide Polymorphisms fromdescriptive term. Such terms could be used
NCBI Build 128 of dbSNP[33] (SNPs
if the gene is not a known gene with an offi(128)) track[38]cial gene symbol. For the gene in question,• Location of repeats found by Repeatthe alternate name, DARPP32, could be
Maskerused or a descriptive term such as NMDA
which is less selective and returns a larger
Gene structure is shown in these tracks withnumber of results.
filled blocks representing exons; thick blocks
3. Enter the gene symbol, PPP1R1B into the are in the coding sequence (CDS) and thinblocks represent untranslated regions (UTRs).
position or search term box (Figure 2).
Clicking on the submit button directs the The lines connecting the blocks are introns.
user to a page displaying the search results. The direction of arrowheads on the lines or the
For each track where there are data items blocks show the strand on which the element recontaining PPP1R1B as their identifier or sides. Right-facing arrows show that it is on thein their description, results are presented sense strand while left-facing arrows show thatas links to the genomic positions of these it is on the antisense strand. To change the senseof the strand in order to more conveniently viewitems. (Figure 3).
annotation on the antisense strand, the Genome
4. Next, click on one of the links, e.g., the Ref- Browser display may be reversed using the reSeq Genes PPP1R1B at chr17:35036705- verse button underneath the Genome Browser
3Fishing for Genes in the UCSC Browser

Searchbox
SelectAssembly
GenomeHome

Genomes

Blat

TablesGene Sorter

PCR

SessionFAQ

Help

Human (Homo sapiens) Genome Browser Gateway
The UCSC Genome Browser was created by the Genome Bioinformatics Group of UC Santa Cruz.
Software Copyright (c) The Regents of the University of California. All rights reserved.

Clade

clade
Vertebrate

genomeHumanassemblyMar. 2006

position or search term
PPP1R1B

image width620

submitClick here to reset the browser user interface settings to their defaults.
add custom tracks

configure tracks and display

clear position

About the Human Mar. 2006 (hg18) assembly (sequences)
The March 2006 human reference sequence (NCBI Build 36.1) was produced by the International Human Genome
Sequencing Consortium.

Assembly
information Sample position queries
Examplequeries

A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST or STS
marker, or a cytological band, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA.
The following list shows examples of valid position queries for the human genome. See the User's Guide for more
information.
Request:Genome Browser Response:

chr7
20p13
chr3:1-1000000
chr3:1000000+2000

Displays all of chromosome 7
Displays region for band p13 on chr 20
Displays first million bases of chr 3, counting from p arm telomere
Displays a region of chr3 that spans 2000 bases, starting with position 1000000

D16S3046

Displays region around STS marker D16S3046 from the Genethon/Marshfield maps. Includes
100,000 bases on each side as well.
RH18061;RH80175 Displays region between STS markers RH18061;RH80175. This syntax may also be used for otherrange queries, such as between cytobands and uniquely-determined ESTs, mRNAs, refSeqs, etc.
AA205474

Displays region of EST with GenBank accession AA205474 in BRCA1 cancer gene on chr 17

AC008101GenomeDisplays
region ofGateway
clone with GenBank
accession
Figure 2: UCSC
Browser
page.
TheAC008101
position or search term box allows
AF083811
Displays region of mRNA with GenBank accession number AF083811
the user to PRNP
search for a position
withintheselected
genomeassembly
orPRNPby keyword, gene
Displays region of genome with HUGO Gene Nomenclature Committee
identifier
NM_017414
Displaystheregionofgenomewith
RefSeqidentifier
NM_017414
symbol or otheridentifier.DisplaysHere,a search for PPP1R1B is being initiated.
NP_059110
the region of genome with protein accession number NP_059110
pseudogene mRNA
homeobox caudal
zinc finger
kruppel zinc finger
huntington
zahlerEvans,J.E.

Lists transcribed pseudogenes, but not cDNAs
Lists mRNAs for caudal homeobox genes
Lists many zinc finger mRNAs
Lists only kruppel-like zinc fingers
Lists candidate genes associated with Huntington's disease
Lists mRNAs deposited by scientist named Zahler
Lists mRNAs deposited by co-author J.E. Evans

Use this last format for author queries. Although GenBank requires the search format Evans JE, internally it uses the format
Evans,J.E..

4

Fishing for Genes in the UCSC Browser

Click here to go to
the location of thelonger splice variant
UCSC Genes
PPP1R1B (uc002hsc.1) at chr17:35038279-35046404 - protein phosphatase 1, regulatory (inhibitor)
PPP1R1B (uc002hsb.1) at chr17:35038279-35046404 - protein phosphatase 1, regulatory (inhibitor)
PPP1R1B (uc002hsa.1) at chr17:35036705-35046404 - protein phosphatase 1, regulatory (inhibitor)
PPP1R1B (uc002hrz.1) at chr17:35036705-35046404 - protein phosphatase 1, regulatory (inhibitor)

RefSeq Genes
PPP1R1B at chr17:35038279-35046404 - (NM_181505) protein phosphatase 1, regulatory (inhibitor)
PPP1R1B at chr17:35036705-35046403 - (NM_032192) protein phosphatase 1, regulatory (inhibitor)

Non-Human RefSeq Genes
PPP1R1B at chr17:35037013-35046370 - (NM_174647) protein phosphatase 1, regulatory (inhibitor)
Ppp1r1b at chr17:35037163-35046403 - (NM_144828) protein phosphatase 1, regulatory (inhibitor)
Ppp1r1b at chr17:35037163-35245015 - (NM_138521) protein phosphatase 1, regulatory (inhibitor)

Human Aligned mRNA Search Results
AF435972 - Homo sapiens dopamine- and cAMP-regulated neuronal phosphoprotein isoform A (PPP1R1B) mRNA, complete cds; alternatively spliced.
AF435973 - Homo sapiens dopamine- and cAMP-regulated neuronal phosphoprotein isoform B (PPP1R1B) mRNA, complete cds; alternatively spliced transcript B1.
AF435974 - Homo sapiens dopamine- and cAMP-regulated neuronal phosphoprotein isoform B (PPP1R1B) mRNA, complete cds; alternatively spliced transcript B2.
AY070271 - Homo sapiens truncated DARPP-32 isoform t-DARPP (PPP1R1B) mRNA, complete cds, alternatively spliced.
BC001519 - Homo sapiens protein phosphatase 1, regulatory (inhibitor) subunit 1B (dopamine and cAMP regulated phosphoprotein, DARPP-32), mRNA (cDNA clone MGC:2855 IMAGE:2987943), complete cds.

Non-Human Aligned mRNA Search Results
AY601872 - Rattus norvegicus, dopamine- and cAMP-regulated phosphoprotein
AY640620 - Mus musculus, DARPP-30a
AY640621 - Mus musculus, DARPP-30b
BC011122 - Mus musculus, protein phosphatase 1, regulatory (inhibitor)
BC026568 - Mus musculus, protein phosphatase 1, regulatory (inhibitor)
BC031129 - Mus musculus, protein phosphatase 1, regulatory (inhibitor)
BC078954 - Rattus norvegicus, protein phosphatase 1, regulatory (inhibitor)
AY890186 - synthetic construct, protein phosphatase 1 regulatory subunit 1B
AY892674 - synthetic construct, protein phosphatase 1 regulatory subunit 1B
AY892675 - synthetic construct, protein phosphatase 1 regulatory subunit 1B
BC118264 - Bos taurus, protein phosphatase 1, regulatory (inhibitor)

Figure 3: Results of a search for PPP1R1B. The results page shows all the tracks that containdata whose annotation includes the keyword “PPP1R1B”. This gene is found in the UCSC
Genes, RefSeq Genes and Human mRNA tracks as well as in the tracks for Non-human RefSeq
Genes and Non-human mRNAs.
image (see Figure 4. The image will then be redrawn so that the 50 to 30 direction of transcription of the antisense gene is from left to right,
which is more intuitive.
Above the Genome Browser image for the human genome assemblies (and for other organisms when available), there is a chromosome
ideogram[13] showing a red box which indicates the position of the current viewing window
within the chromosome. Navigation controls
are found above and below the Browser image(Figure 4). Scrolling down below the Browser
graphic allows access to the visibility controls
for each track grouped by track type (see thelower part of Figure 4). These controls allow
the user to select various tracks for display; display modes can be altered using the pull-down
lists. Visibility options are:arate line, but at 50% of the height of fullmode and without labels• pack which displays several features oneach line with labels• full which shows each feature on a separate
line with labels

Such compacting of tracks is particularly usefulfor those tracks with large amounts of data. By
altering the visibility of a number of tracks, adisplay such as that in Figure 5 can be achieved.
Zooming in to base level in order to examine annotations more closely can be achieved byusing the navigation buttons above the Browser
image. Clicking on the base numbers in the Base
Position track also allows zooming. At the baselevel, the genome bases can be viewed below thenumbering in the Base Position track (Figure 6.
The one-letter amino acid codes for the trans• hide which renders the track invisible
lation of the codon triplets in all three frames• dense which collapses all the features into for the strand being viewed will come into viewa single line
as one zooms to base level (if the Base Position• squish which displays each features a sep- track visibility is full) while codons in various
5Fishing for Genes in the UCSC Browser

Zoom
Home Genomes Blat Tables

Gene Sorter

PCR DNA Convert Ensembl NCBI PDF/PS Session HelpUCSC Genome Browser on Human Mar. 2006 Assembly

Navigate along
the genome

Assembly organismand datemove <<< << < > >> >>> zoom in 1.5x 3x 10x base zoom out 1.5x 3x 10x
jump

position/search chr17:35,036,705-35,046,403

Search box

clear

size 9,699 bp.

configure

Chromosome ideogram

Browser graphic

Click on baseposition tozoom in

Click fortrack
description

move start
< 2.0

>

Click on a feature for details. Click on base position to zoom in around cursor. Click gray/blue bars
on left for track options and descriptions.
default tracks

hide alladd custom tracks

configurereverserefresh

Mapping and Sequencing Tracks

Visibility
Controls

Base Position

Chromosome BandSTS Markers

FISH Clones

dense

hide

hide

hide

hide

Map Contigs

Assembly

Gap

Coverage

BAC End Pairs
hide

hide

hide

hide

hide

Fosmid End Pairs

GC Percent

Short Match

Restr Enzymes

hide

hide

hide

hide

Recomb Rate

Phenotype and Disease Associations

refreshGenes and Gene Prediction Tracks

refreshSpliced ESTs

Human ESTs

Reverses thedisplay for viewing
annotations on
the negative strand

refreshmRNA and EST Tracks
Human mRNAs>

refreshUse drop-down controls below and press refresh to alter tracks displayed.
Tracks with lots of items will automatically be displayed in more compact modes.

Track Groups

move end< 2.0

Other mRNAs

Other ESTs

dense

dense

hide

hide

hide

H-Inv

UniGeneGene Bounds

SIB Alt-Splicing

Poly(A)

hide

hide

hide

hide

hide

Click here for trackdescription

CGAP SAGE
hide

Expression and Regulation

refreshComparative Genomics

refreshVariation and Repeats

refreshENCODE Regions and Genes

refreshFigure 4: Default tracks for the human hg18 (NCBI Build 36.1) assembly at the PPP1R1B gene
locus.

6

Fishing for Genes in the UCSC Browser

Human Mar. 2006 chr17:35,036,705-35,046,403 (9,699 bp)
35040000
Genetic Association Studies of Complex Diseases and Disorders

Window Position
chr17:

A
B

35045000

PPP1R1B
UCSC Gene Predictions Based on RefSeq, UniProt, GenBank, and Comparative Genomics
PPP1R1B
PPP1R1B
PPP1R1B
PPP1R1B
Consensus CDS
CCDS11339.1
CCDS11340.1
RefSeq Genes
PPP1R1B/NM_032192
PPP1R1B/NM_181505
Mammalian Gene Collection Full ORF mRNAs
BC001519
Ensembl Gene Predictions
ENST00000357165
ENST00000254079
ENST00000394271
ENST00000394265
ENST00000394267

C

N-SCAN PASA-EST Gene Predictions
chr17.36.002.a
N-SCAN Gene Predictions
chr17.36.003.a
Exoniphy Human/Mouse/Rat/Dog
Exoniphy
ACEScan alternative conserved Human-Mouse exon predictions
PPP1R1B_pred.1
Human mRNAs from GenBank

DE

Human ESTs That Have Been Spliced
Spliced ESTs
Reported Poly(A) Sites from PolyA_DB

F

p.84152.1
Predicted Poly(A) Sites Using an SVM
NM_181505.polyA-1
NM_032192.polyA-1

G

CpG Islands (Islands < 300 Bases are Light Green)
CpG: 71
SwitchGear Genomics Transcription Start Sites
CHR17_P0438_R1
CHR17_P0438_R2
Genome Institute of Singapore PET of PolyA+ RNA
GIS RNA hES3
Genome Institute of Singapore ChIP-PET
p53 HCT116 +5FU
STAT1 HeLa +gIF
STAT1 HeLa -gIF
cMyc P493
H3K4me3 hES3
H3K27me3 hES3
Regulatory elements from ORegAnno
OREG0024380
OREG0012111
TargetScan miRNA Regulatory Sites

H
I

PPP1R1B:miR-330
Vertebrate Multiz Alignment & PhastCons Conservation (28 Species)
Vertebrate Cons
Chimp
Rhesus
Mouse
Rat
Dog
Cow
Tetraodon
Fugu

J

Simple Nucleotide Polymorphisms (dbSNP build 128)
SNPs (128)
Repeating Elements by RepeatMasker
RepeatMasker

Figure 5: Human hg18 Genome Browser showing multiple annotations for the PPP1R1B gene
locus. Using the track controls below the Browser image, the visibility has been set to display avariety of annotation types in the following tracks: (A) Genetic Association Database (GAD) View;(B) UCSC, CCDS, RefSeq, MGC and Ensembl Genes; (C) N-SCAN predictions and ExoniPhy;(D) ACEScan; (E) Human mRNAs and Spliced ESTs; (F) Poly(A); (G) CpG Islands, SwitchGear
Transcription Start Site predictions, GIS-PET and OregAnno; (H) TargetScan; (I) Conservation;
7and (J) SNPs and RepeatMasker repeats.

Fishing for Genes in the UCSC Browser

5gene annotation tracks are also labeled with the
one-letter amino acid code (Figure 6).

4

Phenotype and Disease
Associations tracks

The Genetic Association Database (GAD) View
track[1] has a red rectangle spanning the
PPP1R1B locus, indicating that this gene has
been associated with a disease or condition (Figure 5, Box A). The details page for this item
shows that the associated condition is nicotine
dependence in certain individuals. Links areprovided to both the GAD database and to thesingle publication documenting evidence for the
association.

Annotation details

Each track has an associated description page
which can be reached either by clicking on thehyperlinked name above the appropriate trackcontrol below this image or via the blue/gray barat the side of the track. The track description details the methods and data sources used to produce the track, validation, credits and citationsof relevant publications. Above the description,
many tracks have configuration controls specificto the track type and some tracks also have filters. These controls allow the user to create thedisplay that best shows the data of interest. Each
item in a track also has a details page which
may be reached by clicking on an item of interest in a track. Instead of configuration controls
in the top section of the page, there are further
details about the track item. These details canbe extensive and may include:

6

Gene and Gene Prediction
tracks

6.1 UCSC GenesThe UCSC Genes[15, 18] track (Figure 5, BoxB) consists of gene models based on data from
GenBank, RefSeq and UniProt, each of which
has a details page that is extremely rich in information about that gene including:• Links to external databases• Confidence scores where applicable• Position information• Links to sequence• Links to alignment information for aligned
sequences,e.g., GenBank sequences.

• Gene descriptions• Database cross-reference links• Alternate gene names• Genetic Association data
• Chemicals interacting with the gene product• Selected microarray data
• mRNA UTR secondary structure• Protein domains and structure• Orthologs from other model organisms• Gene Ontology (GO) annotations• Pathways involving the gene product• Information on the gene model

Annotation data can be noisy, so care must
be taken when using it to make interpretations.
For instance, predictions can contain false positives and experimental data can be erroneous.
For this reason, it is important to evaluate datafrom different sources in order to make an informed judgment as to the confidence that annotations should be assigned. With this in mind,
The UCSC Genes set has four splice variexamples from the different track groups will be ants at the PPP1R1B locus. Two predicted trancompared for the PPP1R1B locus.
scripts encode longer proteins and differ in the8Fishing for Genes in the UCSC Browser

Stop codon

In−frame Met codon

Human Mar. 2006 chr17:35,038,933-35,039,021 (89 bp)
Window Position
chr17:
35038940
35038950
35038960
35038970
35038980
35038990
35039000
35039010
35039020---> C C C T C C A T C T C C T T A G A T C C G G C G C A G G A G A C C A A C G C C T G C C A T G C T G T T C C G G C T C T C A G A G C A C T C C T C A C C A G G T A G G C C C C T C C
P
S
I
S
L
D
P
A
Q
E
T
N
A
C
H
A
V
P
A
L
R
A
L
L
T
R
*
A
P
P
L
P
P
S
P
*
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P
G
R
P
L
P
S
L
H
L
L
R
S
G
A
G
D
Q
R
L
P
C
C
S
G
S
Q
S
T
P
H
Q
V
G
P
S
Genetic Association Studies of Complex Diseases and Disorders
PPP1R1B
UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E
PPP1R1B/uc002hrz.1
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E
PPP1R1B/uc002hsa.1
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P A
PPP1R1B/uc010cvx.1
M
L
F
R
L
S
E
H
S
S
P E
PPP1R1B/uc002hsb.1
M
L
F
R
L
S
E
H
S
S
P E
PPP1R1B/uc002hsc.1
Consensus CDS
CCDS11339.1
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E
CCDS11340.1 M
L
F
R
L
S
E
H
S
S
P E
RefSeq Genes
PPP1R1B/NM_032192
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E
PPP1R1B/NM_181505
M
L
F
R
L
S
E
H
S
S
P E
Mammalian Gene Collection Full ORF mRNAs
BC001519
Ensembl Gene Predictions
ENST00000254079
ENST00000357165
ENST00000394271
ENST00000394265
ENST00000394267
N-SCAN Gene Predictions
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E
chr17.36.003.a
N-SCAN PASA-EST Gene Predictions
I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E
chr17.36.002.a
Exoniphy Human/Mouse/Rat/Dog
Exoniphy
Human mRNAs from GenBank
AF464196
AK127542
AK123112
AK129537
AF435972
CR606470
CR621995
AY070271
AF435973
AF435974
AK024593
AK225058
BC001519
BT007076
Human ESTs That Have Been Spliced
Spliced ESTs
Vertebrate Multiz Alignment & PhastCons Conservation (28 Species)

Right−facing arrow showing
5’−>3’ directionof sequence

Genomesequence
Translation inthree frames

Vertebrate Cons

Sequence level viewof genome inmulitiple alignment

Gaps
+
2
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P EG T AGGCC CC T C C
Human C C C T C C A T C T C C T T A G I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P EG T AGGCC CC T C C
Chimp C C C T C C A T C T C C T T A G I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E G T A G GGC C C T C C
Rhesus C C C T C C T T C T C C T T A G I
R
R
R
R
P
T
P
A
M
L
F
R
V
S
E
H
S
S
P E G T A G GG T C C T C C
Mouse T C C T C C A T C T C T C T A G I
R
R
R
R
P
T
P
A
L
L
F
R
V
S
E
H
S
S
P E G T A G GGC C C T C C
Rat T C C C C C A T C T C C C T A G I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E G T GG G - C C C T C C
Dog C T C C C C A T C T C C T T A G I
R
R
R
R
P
T
P
A
M
L
F
R
L
S
E
H
S
S
P E G T GG GC C C C T C C
Cow C T C C C T G T C T C C T C A G I
Tetraodon = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =Fugu = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =Translation of coding exons in thereading frame of hg18 UCSC Genes

Figure 6: Multiple annotation tracks at the human hg18 PPP1R1B gene locus. At this zoom level,
both the genome sequence and the amino acid translation in three frames are displayed in the Base
Position track at full visibility. On the left side of this track, a right-facing arrow shows that thesequence runs from 50 to 30 . Clicking on the arrow reverse-complements the sequence so that it
reads from right to left (30 to 5p rime). Various gene annotation and alignment tracks show colorcoding at this zoom level; in the mRNA and MGC Genes tracks, by default, the codons are shownas alternating light and dark colored rectangles. The UCSC Genes, CCDS and N-SCAN tracks andthe multiple alignment section of the Conservation track display genomic codons, by default, withthe one-letter amino acids code labeling each codon in the CDS region of each transcript. RefSeq
Genes has this feature switched off by default, but here, it is switched on together with a label foreach item consisting of its gene name and RefSeq accession. At this base-level view, ATG arecodons colored light green and labeled with ”M” to represent potential translation start methionine
codons while stop codons are colored red and are labeled with an asterisk ”*”. The Conservation
track has been configured to show a subset of species alignments and the Vertebrate conservation
scores. These features can be configured using the controls at the top of the description page
reached by clicking on the blue/gray mini-button at the left side of the relevant track.

9

Fishing for Genes in the UCSC Browser

size of an internal exon. The other two transcripts that encode a short protein differ in thelength of the 50 UTR (Figure 5, Box B). Clicking
on the first transcript (UCSC Gene uc002hrz.1)
displays the details page which is divided into
a number of collapsible sections. Selected sections are shown in the UCSC Genes details
page figures: Figure 7 shows sections including those with gene descriptions and alternate
gene names, Figure 8 shows expression data andpathways involving the gene product and Figure
9 shows a section of information about the genemodel for UCSC Gene uc002hrz.1.

6.2 TransMap cross-speciesalignments
The TransMap[35, 36, 44] track contains crossspecies alignments of GenBank[2] mRNAs andSpliced ESTs, RefSeq Genes and UCSC Genes
to the genome. The more sensitive BLASTZ[32] alignment is used to create a base levelprojection of transcript alignments from different species onto a genome in order to predict
orthologous genes on that genome. Mouse,
human and many other vertebrate assemblies
have a TransMap annotation track. For eachgenome, the vertebrate assemblies with BLASTZ
alignments were selected. For closer evolutionary distances, the BLASTZ alignment nets[22]are syntenically filtered to distinguish orthologs
from paralogs; for more distant species or if
synteny is difficult to determine, all BLASTZ
chains[22] are used. In this way, more genes
can be mapped but with the complication thatsome genes are mapped to paralogous regions.
Post-alignment filtering can remove some of the
duplications. It is this set of chains that are used
to create a base-level projection of the transcriptalignments to the genome. The resulting pairwise alignments are shown in Figure 10.

6.3

Other Gene and Gene Prediction
tracksThe RefSeq[31] transcripts are medium blue incolor signifying their Provisional status. At thisstatus level, a RefSeq is represented by a single GenBank source sequence and has not yet
undergone a full review by annotators. During graduation to Reviewed RefSeq status, additional sequence data may be used to modify andextend the transcript structure and additional biological annotations may be added. However,users can make their own judgment by evaluating the additional evidence for a gene structureusing the other annotation data.
The Consensus Coding Sequence (CCDS)
track (Figure 5, Box B) is a high quality
set of annotations consisting of a core set ofprotein-coding regions produced as a collaboration among NCBI, UCSC and the Havana andEnsembl groups at the Wellcome Trust Sanger
Institute (WTSI) and the European Bioinformatics Institute (EBI). CCDS represent a consensus between RefSeq annotations (NCBI) and theEnsembl and Havana annotations (EBI/WTSI).
At this locus, there are CCDS representing
both splice variants in the RefSeq Genes track(NM 032192 and NM 181505) and also, all
the predicted UCSC Genes. The two CCDS
(CCDS11339.1 and CCDS11340.1) represent
all the coding regions that are shown in the Geneand Gene Prediction group annotation tracks in
Figure 5, Box B.
The MGC Genes full-length ORF track has
one MGC clone (BC001519) (Figure 5, Box B).
MGC clone sequences have been submitted to
the GenBank database so the same mRNA also
appears in the Human mRNA track. The mRNAand EST tracks contain BLAT alignments of additional transcripts (see section 7 and Figure 5,
Box E).
The Gene and Gene Predictions group of
tracks also includes gene predictions based on
mRNAs and ESTs such as Ensembl Genes [9](Figure 5, Box B), de novo gene prediction

10

Fishing for Genes in the UCSC Browser(a) Description for UCSC Gene uc002hrz.1
Home

Genomes

Genome Browser

Blat

TablesGene Sorter

PCR

SessionFAQ

Help

Human Gene PPP1R1B (uc002hrz.1) Description and Page Index
Home Genomes
Genome1,Browser
Blat Tables Gene Sorter PCR Session FAQ Help
Description:
protein phosphataseregulatory (inhibitor)
RefSeq Summary (NM_032192): Midbrain dopaminergic neurons play a critical role in multiple brain functions, and

HumanGene PPP1R1B(uc002hrz.1)
Description
and PageIndexabnormal signaling
through dopaminergic
pathways
has been implicatedin several
major neurologic and psychiatricdisorders. One well-studied target for the actions of dopamine is DARPP32. In the densely dopamine- and glutamateHome Genomesphosphatase
Genome1,Browser
Blat Tables Gene Sorter PCR Session FAQ Help
Description:
regulatory(inhibitor)
innervated rat protein
caudate-putamen, DARPP32
is expressedin medium-sized spiny neurons (Ouimet and Greengard, 1990
RefSeqdopaminergic
neurons
playanda criticalrole in 1984
multiplebrain functions,andThe[PubMedSummary
2191086])(NM_032192):
that also expressMidbrain
dopamine
D1 receptors(WalaasGreengard,[PubMed6319627]).
Human
Gene PPP1R1B(uc002hrz.1)
Description
and
Page
Index
abnormalsignaling
throughdopaminergic
pathwayshas
been
implicatedin several
major neurologic
and psychiatricfunction of DARPP32 seems to be regulated by receptor stimulation.
Bothdopaminergic
and glutamatergic(NMDA)
disorders.
One well-studied
targetfor theof dopamine
is DARPP32.
the densely
dopamineandetglutamatereceptor
stimulation
regulatethe extent
of actions
DARPP32
phosphorylation,
but in In
opposite
directions(Halpainal., 1990
Description:
phosphatase1, regulatory(inhibitor)
innervated
rat protein
caudate-putamen,
DARPP32
isstimulation
expressed
in medium-sized
spiny neurons(Ouimetandphosphorylation
Greengard, 1990
[PubMed2153935]).
Dopamine
D1
receptorenhances
cAMP
formation,
resultinginthe
RefSeq Summary(NM_032192):
Midbraindopaminergic
neurons
playanda criticalrole in 1984
multiplebrain functions,
andof[PubMed2191086])that
also
express
dopamine
D1
receptors(WalaasGreengard,[PubMed6319627]).
TheDARPP32(Walaasthroughand Greengard,
1984pathways[PubMedhas
6319627]);
phosphorylated
DARPP32
is a potent
proteinabnormalsignaling
dopaminergic
been
implicatedinseveralmajor
neurologic
andpsychiatricfunctionof DARPP32
seems
to be regulated
by receptor stimulation.
Both dopaminergic
andglutamatergic(NMDA)
phosphatase-1(seeMIM
176875)
inhibitor(Hemmings
et
al.,
1984
[PubMed6087160]).
NMDA
receptorstimulation
disorders.
One well-studied
targetextent
for theof dopamine
is DARPP32.
the densely
dopamineandetglutamatereceptor
stimulation
regulateof actions
DARPP32
phosphorylation,butdephosphorylationin In
opposite
directions(Halpainal., 1990thereby
elevates
intracellular
calcium,the
which
leads
to
and
of phospho-DARPP32,
innervated
rat caudate-putamen,
DARPP32
isactivation
expressedofenhances
incalcineurin
medium-sized
spiny neurons(Ouimetandphosphorylation
Greengard, 1990
[PubMed2153935]).
Dopamine
D1
receptorstimulationcAMP
formation,
resultingin thereducing
thephosphatase-1
inhibitory
activityof
DARPP32(Halpain
et
al.,
1990
[PubMed2153935]).[supplied
by of[PubMed2191086])that
also
express
dopamine
D1
receptors(WalaasandGreengard,
1984[PubMed6319627]).
TheDARPP32 (Walaas and Greengard, 1984 [PubMed 6319627]); phosphorylated DARPP32 is a potent protein
OMIM].
functionof
DARPP32seems
toberegulatedbyreceptorstimulation.
Bothdopaminergic
andglutamatergic(NMDA)
phosphatase-1(see MIM
176875)
inhibitor(Hemmings
et al.,Exon
1984 Count:[PubMed6087160]). NMDA receptor stimulation
Strand:+Genomic
Size:
9700
Exon
Count:
7
Coding7
receptorstimulation regulate
extentof to
DARPP32
butdephosphorylationin opposite directions(Halpain et al., 1990thereby
elevates intracellular
calcium,the
which
leads
activationphosphorylation,of calcineurin andof phospho-DARPP32,mRNA
Secondary
Structureofand 5'UTRs[PubMed2153935]).
Dopamine
D1 receptor
stimulation
enhances
cAMP
formation,
resultingin the phosphorylation
reducing
thephosphatase-1
inhibitory
activityof3'DARPP32(Halpain
et al.,
1990 [PubMed
2153935]).[supplied
by of
DARPP32(Walaasand Greengard,[PubMed6319627]);
phosphorylated
is a potentMicroarray
proteinPage Index
Sequenceand Links1984
UniProt
Comments
Genetic
Associations DARPP32CTD
OMIM].
Press "+" in the
title
bar above
to inhibitor
open this(Hemmings
section.
phosphatase-1(seeMIM
176875)et al.,Exon
1984[PubMedNMDA receptor stimulation
Strand:+ Genomic
Size:
9700Internal
Exon
Count:
CodingCount:
7 6087160]).
(b)and7 external
links
for
PPP1R1B
RNA Structure
Protein
Structure
Other
Species
GO Annotations
mRNA Descriptions Pathways
elevates intracellular calcium, which leads to activation of calcineurin and dephosphorylation of phospho-DARPP32, thereby
Other Names
Model Information
Methodsof DARPP32 (Halpain et al., 1990 [PubMed 2153935]).[supplied by
reducing
the phosphatase-1
inhibitory activity
andLinks
Structure
PageProtein
Index Domain
Sequence and
UniProt Information
Comments Genetic Associations CTD
Microarray
OMIM].
Strand:+ Genomic
Size:
9700 ExonCount:
7 Coding
Count: 7 mRNA Descriptions Pathways
RNA Structure
Protein
Structure
Other
Species
GOExonAnnotations
Press "+" in the title bar above to open this section.
Sequence and Links to Tools and Databases
Other Names Model Information Methods
Page Index Sequence and Links UniProt Comments Genetic Associations CTD
Microarray
Genomic
Sequence (chr17:35,036,705-35,046,404)mRNA (may differ from genome) Protein (204 aa)
in Other
RNA Orthologous
Structure ProteinGenes
Structure
OtherSpecies
Species
GO Annotations
mRNA Descriptions Pathways
GeneSequence
SorterProteome
Browser VisiGene
Table Schema CGAP
andGenome
LinksBrowser
to Tools
and Databases
Other
Names
Press "+"
in the Model
title barInformation
above to openMethods
this section.
EnsemblEntrez Gene
ExonPrimer
GeneCards
Gepis Tissue
H-INV
Genomic Sequence (chr17:35,036,705-35,046,404)mRNA (may differ from genome) Protein (204 aa)
HGNC
HPRD
HuGE
Jackson Labs OMIM
PubMedGene(GO)with Structured
GeneSequence
Sorter Ontology
BrowserProteome
Browser
VisiGene Vocabulary
Table Schema CGAP
andGenome
Links
to Annotations
Tools
and Databases
Stanford SOURCE
Treefam
UniProt
EnsemblEntrez Gene
ExonPrimer
GeneCards
Gepis Tissue
H-INV
Molecular Function:
Genomic Sequence (chr17:35,036,705-35,046,404)mRNA (may differ from genome) Protein (204 aa)
HGNC
HuGE
Jackson Labs OMIM
PubMed
GO:0004860 proteinHPRD
kinase inhibitor activity
Comments
andDescription
Text
from
UniProt(Swiss-Prot/TrEMBL)
Gene
Sorter protein
GenomeBrowserProteome
Browser
VisiGene
Table Schema CGAP
GO:0004864
phosphataseinhibitor
activity
Stanford
SOURCE Treefam
UniProt
EnsemblEntrez Gene
ExonPrimer
GeneCards
Gepis Tissue
H-INV
ID:
IPPD_HUMAN
Biological
Process:
HGNC
HPRD and cAMP-regulated
HuGE
JacksonLabs OMIM
PubMedDESCRIPTION:
Dopamineneuronal
phosphoprotein(DARPP-32).
signaltransduction
GO:0007165
Comments
andText from UniProt (Swiss-Prot/TrEMBL)
FUNCTION:
Inhibitor
ofDescription
protein-phosphatase
Stanford SOURCE
Treefam
UniProt1. Description for PPP1R1B(c)
UniProt
SUBCELLULAR LOCATION: Cytoplasm.
CellularComponent:
ID:
IPPD_HUMAN
PTM:
Dopamine- and cyclic AMP-regulated neuronal phosphoprotein.
GO:0005737 cytoplasm
DESCRIPTION:
DopamineandiscAMP-regulated
neuronal
phosphoprotein (DARPP-32).
PTM: Phosphorylation
Thr-34required for activity(By similarity).
Comments
andofDescription
Text from
UniProt(Swiss-Prot/TrEMBL)
FUNCTION:
Inhibitor
1. inhibitor
SIMILARITY:
Belongsoftoprotein-phosphatasethe protein phosphatase
1 family.
SUBCELLULAR LOCATION: Cytoplasm.
ID:
IPPD_HUMAN
PTM: Dopamine- and cyclic AMP-regulated neuronal phosphoprotein.
DESCRIPTION:
DopamineandisassociatedcAMP-regulated
neuronal
phosphoprotein (DARPP-32).
Descriptions
from
all
GenBankmRNAs
PTM:Genetic
Phosphorylationof Thr-34
required
activity(By
similarity).
Association
Studiesof forComplex
Diseasesand Disorders
FUNCTION:
Inhibitor
1. inhibitor 1 family.
SIMILARITY:
Belongsoftoprotein-phosphatasethe protein phosphatase
Press "+" in the title
bar above to open
this section.
SUBCELLULAR
LOCATION:
Cytoplasm.
Genetic Association Database: PPP1R1B
PTM:
Dopamineand cyclic
AMP-regulated
neuronal phosphoprotein.
CDC HuGE
Published
Literature:
PPP1R1B
PTM:
Phosphorylationof Thr-34
isnicotine
requiredfor
activity(By
similarity).
Genetic
Association
StudiesofsmokingComplex
Diseasesand Disorders
Positive
DiseaseAssociations:behavior
Biochemical
and Signaling Pathways
SIMILARITY:
RelatedStudies:Belongs to the protein phosphatase inhibitor 1 family.
Genetic Association Database: PPP1R1B
BioCarta
NCI Cancer
GenomeAnatomy Project
CDC
HuGEfrom
Published
Literature:
PPP1R1B
1. Genetic
nicotine smoking
behavior
h_ck1Pathway- Regulation
ofStudies
ck1/cdk5
byComplex
type 1behavior
glutamate
receptors
Association
Diseasesand Disorders
Positive
DiseaseAssociations:nicotineof
smoking(d) Alternate
names
for PPP1R1B
h_fosbPathway- FOSBgene
expression
and drug
abuse
Beuten,J. etal. 2006,
Association
analysisof theprotein phosphatase1 regulatory subunit 1B (PPP1R1B) gene withRelatedStudies:
Genetic
Association
Database:
PPP1R1B
nicotine
dependencein Europeanand African-American smokers, Am J Med Genet B Neuropsychiatr Genet 2006.
CDC HuGE Published Literature: PPP1R1B
1. OthernicotineNamessmokingfor
behavior
Thisnicotine
Gene smoking behavior
Positive
Disease Associations:Beuten,J. et al. 2006, Association analysis of the protein phosphatase 1 regulatory subunit 1B (PPP1R1B) gene withRelatedStudies:
Alternate
Gene
Symbols:
DARPP32,and
IPPD_HUMAN,
NM_032192,
NP_115568,
Q9UD71Genet 2006.
nicotine
dependencein EuropeanAfrican-American
smokers, Am
J Med GenetQ9H7G1,
B Neuropsychiatr
UCSC ID: uc002hrz.1
1. nicotine smoking behavior
RefSeq Accession: NM_032192
Beuten,J. et al.(aka2006,
Association analysis of the protein phosphatase 1 regulatory subunit 1B (PPP1R1B) gene withProtein:
Q9UD71
IPPD_HUMAN)
nicotine
dependence in European- and African-American smokers, Am J Med Genet B Neuropsychiatr Genet 2006.
CCDS:
CCDS11339.1

Figure 7: Description,
links Informationand gene names from the details page for the human gene PPP1R1B
Gene Model(uc002hrz.1) in category:
the UCSC Genes
set. (a) shows the RefSeq Genes description for the gene. (b)coding nonsense-mediated-decay: no RNA accession: NM_032192.2
shows links to theon thedetails
next
links to various tools
exonsections
count:
7 CDS
single inpage.
3' UTR: The
no RNA
size:section contains
1841
ORF
size:
615
CDS
singleinintron:no
Alignment%
ID:
100.00and databases both at UCSC and externally. (c) shows a section containing the UniProt/SwissProt
txCdsPredict score: 1416.67 frame shift in genome:% Coverage:
100.00
database description
for the protein encoded by thisnogene.
The UniProt
ID (IPPD HUMAN) links
has start codon:
yesstop codon in genome:
no # of Alignments:
1
to the UniProt database
entry yesfor a retained
proteinisoform producedby this gene.
UniProt record also
has end codon:
intron:no # AT/AC introns
0 The
Generatedby www.PDFonFly.com
has information about other protein isoforms represented in the database. (d) shows a section ofalternate names for the PPP1R1B gene, some of11which have links to external databases.

Fishing for Genes in the UCSC Browser
Comparative Toxicogenomics Database (CTD)(a) this
Microarraydata for PPP1R1B
Press "+" in the title bar above to open
section.
Microarray Expression Data
Expression ratio colors: red high/green low

SubmitGNF Expression Atlas 2 Data from U133A and GNF1H Chips

RatiosAbsolutemRNA Secondary Structure of 3' and 5' UTRs
Press "+" in the title bar above to open this section.

RatiosAbsolute

Protein Domain and Structure Information
Press "+" in the title bar above to open this section.

Orthologous Genes in Other Species
Press "+" in the title bar above to open this section.

Gene Ontology (GO) Annotations with Structured Vocabulary
Molecular Function:
Ratios
GO:0004860 protein kinase inhibitor activity Absolute
GO:0004864 protein phosphatase inhibitor activity

Affymetrix All Exon Microarrays
Biological Process:GO:0007165 signal transduction
Cellular Component:
GO:0005737 cytoplasm

RatiosAbsolute

Descriptions from all associated GenBank mRNAs(b) this
Pathways
involving PPP1R1B
Press "+" in the title bar above to open
section.
Biochemical and Signaling Pathways
BioCarta from NCI Cancer Genome Anatomy Project
h_ck1Pathway - Regulation of ck1/cdk5 by type 1 glutamate receptors
h_fosbPathway - FOSB gene expression and drug abuse

Other Names for This Gene

Figure 8: Expression data and pathways sections from the details page for the human gene
Alternate Gene Symbols: DARPP32, IPPD_HUMAN, NM_032192, NP_115568, Q9H7G1, Q9UD71
PPP1R1B (uc002hrz.1)
in the UCSC Genes set. (a) shows heatmap displays of microarray exUCSC ID: uc002hrz.1
RefSeq Accession: NM_032192
pression data forProtein:
PPP1R1B
in a variety of tissues and cell lines. The upper dataset is from theQ9UD71 (aka IPPD_HUMAN)
CCDS: of
CCDS11339.1
Genomics Institutethe Novartis Research Foundation (GNF) (http://symatlas.gnf.org) using
Affymetrix chips. The lower dataset was provided by Affymetrix (http://www.affymetrix.com)
Gene Model Informationand it was produced using Affymetrix Human Exon 1.0 ST arrays. (b) is the pathways section
category:codingnonsense-mediated-decay:RNA
accession: NM_032192.2
which has links to
the BioCarta
pathways
involving
the
PPP1R1B
gene product.
12 noexon count:
7 CDS single in 3' UTR:
no RNA size:
1841
ORF size:

615 CDS single in intron:

txCdsPredict score: 1416.67 frame shift in genome:

no Alignment % ID:

100.00no % Coverage:

100.00Other Names for This Gene
Alternate Gene Symbols: DARPP32, IPPD_HUMAN, NM_032192, NP_115568, Q9H7G1, Q9UD71
UCSC ID: uc002hrz.1
RefSeq Accession: NM_032192
Protein: Q9UD71 (aka IPPD_HUMAN)
CCDS: CCDS11339.1

Fishing for Genes in the UCSC Browser

Gene Model Information
category:codingnonsense-mediated-decay: no RNA accession: NM_032192.2

exon count:

7 CDS single in 3' UTR:

ORF size:

615 CDS single in intron:no RNA size:

1841

no Alignment % ID:

100.00txCdsPredict score: 1416.67 frame shift in genome:

no % Coverage:

100.00has start codon:

yesstop codon in genome:

no # of Alignments:

1

has end codon:

yesretained intron:no # AT/AC introns0selenocysteine:noend bleed into intron:

0 # strange splices:0

Click here for a detailed description of the fields of the table above.

Methods, Credits, and Use Restrictions

Figure 9: Gene model information section from the UCSC Genes details page for the human gene
Click here for details on how this gene model was made and data restrictions if any.
PPP1R1B (uc002hrz.1).
This section shows that uc002hrz.1 is protein-coding, has seven exonsand has an open reading frame (ORF) of 615 bp among other features.
tracks such as N-SCAN, and exon prediction
tracks such as ExoniPhy (Figure 5, Box C).
E XONI P HY uses conservation among human,
mouse, rat and dog to identify putative proteincoding exons. Computational gene predictions
can provide validation for the gene and transcript structures produced by manual curation
efforts such as those in the RefSeq Genes andVega Genes[41] tracks.

7

GenBank mRNA and EST
sequence alignments

The mRNA and EST Tracks group (Figure 5,
Box E) show sequences from GenBank thatalign well to the genome using BLAT. In Figure 5, these tracks are compacted; the HumanmRNAs track is shown with the visibility set tosquish and the Spliced ESTs track is in dense
mode (see the paragraph on track visibility insection 3). The transcript sequence alignments
are regularly updated to keep in synchrony with
GenBank; mRNA and RefSeq Genes updates aredaily and ESTs tracks are updated weekly. The
mRNA and EST transcripts may suggest the existence of additional exons and therefore additional transcript variants than those found in thegene and gene prediction tracks. The Spliced
ESTs track shows that there are ESTs at the
PPP1R1B locus that have two additional small

exons towards the 30 end of the gene (Figure 5).
ESTs can therefore be used to predict the existence of additional splice forms not represented
by mRNAs. Sequence data can be noisy; in particular, ESTs tend to have low sequence quality
and were generated by single-pass sequencing.
Therefore, care should be taken in interpretingthese data. One caveat is that differences between transcripts and the reference genome may
not be noise, but simply genetic variation between individuals. The SNPs track can indicate
such instances (Figure 5, Box J and Figure 11).
The SNPs track may display no known SNPs
from dbSNP[33] at the position of the nonsynonymous codon. It may be that this is a SNP
that has not yet been discovered or submitted
Generated by www.PDFonFly.com
to dbSNP or it could be due a sequencing error resulting in an incorrect base call. Without
evidence of a SNP or viewing the sequencing
quality scores, it is impossible to determine theorigin of this base change.
There are configurable signals in the alignment displays for the mRNAs and ESTs trackthat denote certain features in the sequences andmay aid in the identification of noise in the sequences:

13• By default, the mRNAs tracks display red
or yellow lines in aligned blocks where abase difference between a transcript and thereference genome results in a nonsynonymous codon (Figures 11(b) and (c). At

Fishing for Genes in the UCSC Browser

Window Position
chr17:

35038000

35039000

Human Mar. 2006 chr17:35,036,705-35,046,403 (9,699 bp)
35040000
35041000
35042000
35043000
35044000
UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics

35045000

35046000

PPP1R1B/uc002hrz.1
PPP1R1B/uc002hsa.1
PPP1R1B/uc010cvx.1
PPP1R1B/uc002hsb.1
PPP1R1B/uc002hsc.1
RefSeq Genes
PPP1R1B/NM_032192
PPP1R1B/NM_181505
Mammalian Gene Collection Full ORF mRNAs
BC001519
TransMap UCSC Gene Mappings

A

Mouse uc007lfz.1

B

Rat NM_138521.1
Mouse NM_144828.1

C

Rat AY601872.1
Mouse BC026568.1
Rat BC078954.1
Mouse BC011122.1
Mouse BC031129.1
Marmoset DQ535487.1
Mouse AB221544.1

Mouse uc007lga.1
Mouse uc007lgb.1
TransMap RefSeq Gene Mappings

TransMap GenBank mRNA Mappings

Mouse AY640620.1
Mouse AY640621.1
Mouse AK005627.1
Mouse AK141563.1
Mouse AF281662.1
Rhesus AF233348.1
Rat AF281661.1
Ensembl Gene Predictions
ENST00000254079
ENST00000357165
ENST00000394271
ENST00000394265
ENST00000394267
Human mRNAs from GenBank
AF464196
AK127542
AK123112
AK129537
AF435972
CR606470
CR621995
AY070271
AF435973
AF435974
AK024593
AK225058
BC001519
BT007076
BX648641
AK123950
AK124417
AF233349
BC118070
BC122554
Human ESTs That Have Been Spliced
Spliced ESTs

Figure 10: TransMap track at the human hg18 PPP1R1B gene locus. (A) UCSC Genes; (B) RefSeq
Genes and (C) GenBank mRNAs alignments from other species are projected on to the humangenome via BLASTZ alignment chains and nets. The TransMap ESTs and human mRNAs are shownin squish visibility mode since there are large numbers of these transcripts. For the same reason,
human Spliced ESTs are shown with dense visibility. Colored lines on the alignments represent
nonsynonymous codons in aligned transcripts compared to the reference genome sequence; redsignifies that amino acids differ in physicochemical properties and yellow signifies similar aminoacids. TransMap alignments show that the exons towards the 30 end of the PPP1R1B gene appear
to be fast evolving in human whereas those at the 50 end are evolving at a slower rate.

14

Fishing for Genes in the UCSC Browser(a) Full view of mouse Vill gene with nonsynonymous base changes in MGC and mRNA tracks
Window Position
chr9:118965000

Mouse July 2007 chr9:118,961,920-118,980,444 (18,525 bp)
118970000
118975000
RefSeq Genes

118980000

Vill/NM_011700
Mammalian Gene Collection Full ORF mRNAs

Nonsynonymous basesubstitution changes
colored red and yellow

BC021808
BC022664
Mouse mRNAs from GenBank
AK028229
AK166823
BC021808
AJ344341
BC022664
AK166652
AK188903
Simple Nucleotide Polymorphisms (dbSNP build 128)

U72681

SNPs (128)(b) Exon 5 showing genomic codons and known SNPs resulting in nonsynonymous base changes
Window Position
chr9:
--->

Nonsynonymousbase substitutions
coincide with SNPs

118969300

Mouse July 2007 chr9:118,969,225-118,969,800 (576 bp)
118969400
118969500
118969600
118969700

RefSeq Genes
Vill/NM_011700
Mammalian Gene Collection Full ORF mRNAs
BC021808
Mouse mRNAs from GenBank
AK028229
AK166823
BC021808
AJ344341
Simple Nucleotide Polymorphisms (dbSNP build 128)
SNPs (128)

Nonsynonymous SNPs from dbSNP (NCBI build 128)(c) Base-level view of exon 5 showing amino acid substitutions caused by nonsynonymous base changes
Nonsynonymous basesubstitution changes
Arg to Lys
Mouse July 2007 chr9:118,969,487-118,969,550 (64 bp)
Window Position
118969500
118969510
118969520
118969530
118969540
chr9:---> T G C T C T C A A G T T T G C G G A G A C C A A C A T G T A C A A T G T C C A G C G A C T G C T T C A C A T C A G G G G A A G G
L
L
S
S
L
R
R
P
T
C
T
M
S
S
D
C
F
T
S
G
E
G
C
S
Q
V
C
G
D
Q
H
V
Q
C
P
A
T
A
S
H
Q
G
K
E
S
A
L
K
F
A
E
T
N
M
Y
N
V
Q
R
L
L
H
I
R
G
R
Nonsynonymous base
RefSeq Genes
substitution changes Vill/NM_011700S A L K F A E T N M Y N V Q R L
L
H
I
R
G
R
Mammalian Gene Collection Full ORF mRNAs
Phe to Leu
BC021808
L
K
Mouse mRNAs from GenBank
AK028229
AK166823
BC021808
LK
AJ344341
K
Simple Nucleotide Polymorphisms (dbSNP build 128)
SNPs (128)

Known SNPs from dbSNP (NCBI build 128)

Figure 11: Genome Browser transcript rendering modes: Non-synonymous base changes. Various
signals can be incorporated into the track displays that can aid in identifying noise in the data. The
mouse (mm9, NCBI Build 37 assembly) Vill gene is shown at different zoom levels. Colored tickmarks (zoomed out) or rectangles (base level view) represent nonsynonymous amino acid changes
due to substitutions in MGC Genes and mRNA transcripts compared to the reference genome.
Similar amino acids are colored yellow and amino acids that differ in physicochemical propertiesare colored red. Zooming in to a specific region can be achieved by clicking at the top of theBase Position track or using the zoom controls. (a) shows the entire Vill gene. (b) shows exon 5
with genomic codons appearing in the Base Position track and the RefSeq Genes, MGC and mRNA
tracks. The nonsynonymous base changes in BC021808 and in the AJ344341 are due to known
polymorphisms colored red in the SNP track. (c) shows the base level view of exon 5.
15

Fishing for Genes in the UCSC Browser

the base level display, the nonsynonymouscodons in the transcripts display the one
letter amino acid codes (Figure 11(c)).
• By default, the ESTs tracks display redlines in aligned blocks showing a base difference between a transcript and the reference genome; this signal can also be turned
on for mRNAs and MGC Genes.
• Vertical blue lines indicate an insertion at
the beginning or the end of a transcript relative to the reference genome (Figure 12(a)).
• Green lines indicate the presence of apolyA tail at the 30 end of a transcript (Figure 12(a)).
• Orange lines indicate insertions in the middle of a transcript relative to the reference
genome (Figure 12(b)).
• Double horizontal lines indicate that both
the genome and the transcript have an insertion. This may be due to poor sequencequality in a subregion of the transcript (Figures 12(a) and (b)).
Due to technical reasons, cloned sequences
are often incomplete especially at the ends of
the UTRs. Therefore, it is difficult to determine
whether differences in UTR length are due to”real” variation between transcripts. Genomic
data displayed in the Genome Browser can help
the user to make an informed decision regarding
the completeness of mRNAs. A vertical green
line at the 30 end of a transcript indicates thepresence of a polyA tail, confirming that the sequence is complete at the 30 end. Both reported
and predicted polyadenylation (polyA) sites areshown in the Poly(A) track[4, 24]; data in thistrack may suggest alternative polyadenylationsites whose use would result in variation of the
30 UTR length (Figure 5, Box F). For PPP1R1B,
both predicted and reported sites are in agreement and coincide with the 30 ends of the transcripts at this locus.
The completeness of the 50 UTR is moredifficult to assess. To aid in this evaluation, there are computationally predicted sites

for transcription start sites (TSS) (Eponine
TSS [8] and SwitchGear TSS (http://www.
switchgeargenomics.com/) tracks). In Figure
5, Box G, the SwitchGear Genomics TSS track
predicts the transcription start sites of both thelonger and shorter splice variants in the RefSeq Genes and Ensembl Genes tracks (Box B).
Experimental data such as ditags can be used
to support and verify the 50 and 30 ends of atranscript. Gene Identification Signature PairedEnd Tags (GIS-PET) [5, 6, 30, 40, 43] involves the sequencing of 50 and 30 signaturesof full-length cDNAs that are subsequently concatenated to form ditags, sequenced and thenmapped to the genome of origin to mark theboundaries of the transcripts (Figure 5, Box
G and Figure 14). Ditags offer a much more
efficient way of obtaining such data than traditional cDNA sequencing with the limitationthat the internal exon structure is not determined. GIS-PET data from human embryonicstem cells (hES3) confirm the existence of transcripts whose 50 end is coincident with both the
50 end of the longer and shorter PPP1R1B transcripts (NM 181505) and with the 50 end ofsome of the longer mRNAs (Figure 14). At the
30 end, there are ditags that are coincident thethe 30 end of the RefSeq transcripts and manymRNA transcripts of the PPP1R1B gene (Figure 14) as well as the computationally predicted
SwitchGear TSSs.

8

Conservation andregulation data

The Conservation track shows a 28-way multiple alignment of vertebrate genomes[29] created using the MULTIZ alignment program[3]and a histogram (wiggle type track) of conservation scores[34] associated with the alignment(Figure 5, Box I). Conservation tends to peak incoding regions of the gene and falls off in noncoding parts (introns and intergenic regions) so

16

Fishing for Genes in the UCSC Browser(a) Insertions at the end of transcripts and polyA tails
Human Mar. 2006 chr17:35,045,550-35,046,460 (911 bp)
35046000

Window Position
chr17:--->

RefSeq Genes
PPP1R1B/NM_032192
PPP1R1B/NM_181505
Mammalian Gene Collection Full ORF mRNAs
BC001519
Human mRNAs from GenBank
AF464196
AK127542
AK123112
AK129537
AF435972
CR606470
CR621995
AY070271
AF435973
AF435974
AK024593
AK225058
BC001519
BT007076
BX648641
AK123950
AK124417
BC118070
BC122554

PolyA tails

Insertion at
end of mRNA(b) Internal transcript insertions
158362000

Mouse July 2007 chr1:158,357,727-158,362,861 (5,135 bp)
158361000
158360000
RefSeq Genes

158359000

Window Position:chr1
Soat1/NM_009230

Mammalian Gene Collection Full ORF mRNAs
BC083092
Mouse mRNAs from GenBank
L42293

AK018442
AK142486
DQ903181
AK087210

BC083092
AK052299
AK159393
AK159529
AK160017
S81092
U06668Internal insertions
in transcripts

Figure 12: Genome Browser transcript rendering modes: Insertions and polyA tails. Various
signals can be incorporated into the track displays for GenBank mRNAs and ESTs that can
aid in identifying noise in the data. (a) shows the human PPP1R1B gene locus with vertical,
colored lines at the 30 ends of mRNAs; blue indicates insertions (at the 50 or 30 transcript end)in the transcript alignment relative to the genome and green lines indicate the presence ofpolyA tails. (b) shows the mouse (mm9, NCBI Build 37 assembly) Soat1 gene locus showing
orange lines in aligned mRNAs which indicate insertions that occur in the middle of themRNA sequences in their alignments to the genome. Note that Soat1 is on the reverse strand
and the image has been reversed using the reverse button below the Genome Browser graphic(see Figure 4) so the gene can be viewed in the 50 to 30 orientation. Track element labels arenow shown on the right side of the image.

17

Fishing for Genes in the UCSC Browser(a) Insertion in both transcript and genome
Genome and transcript both have insertions
Human Mar. 2006 chr15:43,267,047-43,267,092 (46 bp)
Window Position
43267090
43267085
43267080
43267075
43267070
43267065
43267060
43267055:chr15C C G C C C T C G C C A C C C C T G T C G C C C C C G G A C C C A C G C C G C C C C C G C G --->
P
P
S
P
P
L
S
P
P
D
P
R
R
P
R
R
R
P
R
H
P
C
R
P
R
T
H
A
A
P
A
A
A
L
A
T
P
V
A
P
G
P
T
P
P
P
R
Consensus CDS
CCDS10120.2
RefSeq Genes
SHF/NM_138356
Human ESTs That Have Been Spliced
BX446958
BX446025
AL529700
BX438306
BX332806
BX423813
BX352799
BX421607
BX457975
BI915484
DA061244
BX442519
BX441951
DA065885
DA017657
DC412792
DC396888(b) EST sequence indicating sequence that is unalignable to the genome

EST sequence unaligned tohuman hg18 genome sequence

Figure 13: Genome Browser transcript rendering modes: Insertions in both sides of the alignment.
Various signals can be incorporated into the track displays for GenBank mRNAs and ESTs that
can aid in identifying noise in the data. (a) shows the human (hg18, NCBI Build 36.1) SHF gene
locus at a position where the human EST, AL529700, has double horizontal lines between theblack rectangles representing sequence aligned to the genome. The double lines indicate that there
are insertions in the alignment in both the EST sequence and the genome. This is shown in (b)where the AL529700 sequence is blue if it aligns to the genome where black text shows unaligned
regions. The unaligned sequence in the red box corresponds to the double lines in image in (a)where it can also be noted that the genome sequence in this region is different from that in thehuman EST sequence whereas the flanking regions from both sequences are similar, hence theinsertion in both transcript and genome in the sequence alignment. This region of the EST is likely
to be an erroneous sequence as a result of poor quality sequencing.

18

Fishing for Genes in the UCSC Browser

Human Mar. 2006 chr17:35,036,400-35,038,600 (2,201 bp)
35037000
35037500
35038000
UCSC Gene Predictions Based on RefSeq, UniProt, GenBank, and Comparative Genomics

Window Position
chr17:

35038500

PPP1R1B
PPP1R1B
PPP1R1B
PPP1R1B
RefSeq Genes
PPP1R1B/NM_032192
PPP1R1B/NM_181505
Mammalian Gene Collection Full ORF mRNAs
BC001519
N-SCAN PASA-EST Gene Predictions
chr17.36.002.a
N-SCAN Gene Predictions
chr17.36.003.a
Human mRNAs from GenBank
AF464196
AK127542
AK123112
AK129537
AF435972
CR606470
CR621995
AY070271
AF435973
AF435974
AK024593
AK225058
BC001519
Human ESTs That Have Been Spliced
Spliced ESTsCpG Islands (Islands < 300 Bases are Light Green)
CpG: 71
Genome Institute of Singapore PET of PolyA+ RNA (embryonic stem cell hES3)290659-1-1
292622-1-5332791-1-1
353951-1-4
413608-1-1
406135-1-1
256264-1-1
532454-3-1
401956-1-1
433582-1-3425529-1-2
5’ PET tags
36150-1-10
184616-1-3
supporting
96706-1-1
171432-1-2
AK127542 andother long mRNAs 369073-1-1
197364-1-4170059-1-5
518216-1-1
220273-1-1
455226-1-1
424563-1-1
393455-1-1
5109-1-7

5’ PET tags supporting
AY070271 and othershorter mRNAs

Figure 14: PPP1R1B locus showing the GIS-PET PolyA+ RNA ditags from the human embryoniccell line (hES3). The GIS-Pet (Gene Identification Signature Paired End Ditags) RNA track can beconsidered in evaluating the 50 completeness of transcripts. By clicking on the zoom buttons above
the Browser image or by clicking above the base numbers at the top of the image, a zoomed-in
genome view can be created. The GIS-Pet RNA track shows ditags from the 50 and 30 ends offull-length polyA+ mRNA. In this view, it can be seen that there are ditags whose 50 end coincidewith the 50 end of some of the longer mRNAs e.g. AK127542 and AK123112 and ditags thatcoincide with the 50 end of the shorter mRNAs, e.g., AY070271 and AF435973 and the RefSeq,
NM 181505. There is a longer mRNA (AF464196) and ESTs that have been used to extend the
RefSeq, NM 181505, further upstream, but there are no ditags that represent this transcript.
19

Fishing for Genes in the UCSC Browser

it is a strong signal for a protein-coding gene
(Figure 15). Conservation of sequence implies
functional significance and can also occur where
there are regulatory elements in the genome.
The ACEScan[42] track predicts conserved
alternative exons that are present in some transcripts and skipped by others in both human andmouse (Figure 5, Box D). Enrichment of splicing regulatory motifs occurs in intron regions
close to alternative exons, which also show agreater degree of conservation than those close
to constitutive exons. ACEScan uses this information to predict the constitutive exon that isskipped in the human mRNA, AK129537.
Transcriptional regulatory elements tend to beenriched near the first exon [27]. Evidence ofsuch motifs are the CpG island [10] at the 50 endof the PPP1R1B gene locus and the SwitchGear
TSS prediction[7, 39] which is color-coded according to confidence level (a darker color implies a higher score) (Figure 5, Box G). The
ORegAnno[11] track displays hand-curated regulatory regions extracted from the literature(Figure 5, Box G). The darker green rectangle
represents a regulatory region, located in an intron of the PPP1R1B, bound by the CCCTCbinding factor (zinc finger protein) (CTCF) transcription factor. The lighter green item below represents the actual location of the CTCF
binding site. This binding site was determinedby ChIP (Chromatin ImmunoPrecipitation)-chip
experiments (details are found by clicking onthese track items). Histone modifications andmultiple transcription factor binding sites for avariety of cell types are shown in the GIS-PET
track (the GIS-PET method is described in section 7). Tri-methylation of lysine4 and lysine27
on histone H3 is indicated at the 50 end of the
PPP1R1B gene (Figure 5, Box G). Such signals for regulatory elements may be misleading;CpG islands are frequently found in or near promoters of genes but not all genes have them,
TSS predictions may contain false positives andtranscription factor binding site measurements
can be noisy.

TargetScan[12, 25, 26] predicts the presenceof a microRNA binding site in a conserved region at the 30 end of the transcript (Figure 5, Box
H). The prediction is based partially on conservation so the TargetScan annotation and conservation are not independent evidence of a regulatory region.
The Conservation track shows peaks of conservation that correspond to the coding sequenceof the gene (Figure 5, Box I). Conservation falls
off at the exon/intron boundaries as illustrated
in Figures 15(a) and (b) which show a close-up
view of the 50 and 30 ends of the PPP1R1B gene.
At this zoom level, by default, the Conservation track shows the nucleotide sequence of
the aligned genomes, and, in coding regions
based on the longest UCSC Genes transcript at
this locus, the codon translation can be seen foreach of the genomes. This enables the user
to see not only the conservation at the aminoacid level but also where there are differences at
the amino acid level between proteins encodedby orthologous protein-coding genes. In Figure15(b), it is possible to see that there is a SNP(rs35797948) in the SNPs (128) track which iscolored red, indicating a nonsynonymous mutation in the coding region. Clicking on the
SNP in this track displays further information
about this SNP and a link out to the entry for
the SNP in dbSNP at NCBI (http://www.ncbi.
nlm.nih.gov/SNP/). This reveals that there are
two known alleles (A/G) which code for either
an arginine (CGC codon) or a histidine (CAC)
amino acid in the translation of this last codingexon of PPP1R1B. Histidine and arginine areboth positively charged making this a conservative substitution; histidine is an aromatic structure.

9

Ordering an MGC clone

Having used the Genome Browser to explore the
PPP1R1B gene, the user may now desire to order a clone for this gene for experimental re-20

Fishing for Genes in the UCSC Browser(a) 50 view
Window Position
chr17:--->

35039000

35039050

35039100

35039150

Human Mar. 2006 chr17:35,038,914-35,039,613 (700 bp)
35039200
35039250
35039300
35039350

35039400

35039450

35039500

35039550

35039600

UCSC Gene Predictions Based on RefSeq, UniProt, GenBank, and Comparative Genomics
PPP1R1B
PPP1R1B
PPP1R1B
PPP1R1B
Consensus CDS
CCDS11339.1
CCDS11340.1
RefSeq Genes
PPP1R1B/NM_032192
PPP1R1B/NM_181505
Mammalian Gene Collection Full ORF mRNAs
BC001519
Vertebrate Multiz Alignment & PhastCons Conservation (28 Species)
Vertebrate Cons
Chimp
Rhesus
Mouse
Rat
Dog
Cow
Tetraodon
Fugu
Simple Nucleotide Polymorphisms (dbSNP build 128)

Conservation falls off
at exon/intron boundaries(b) 30 view
Window Position
chr17:--->

35045250

35045300

35045350

35045400

35045450

Human Mar. 2006 chr17:35,045,192-35,045,891 (700 bp)
35045500
35045550
35045600
35045650

35045700

35045750

35045800

35045850

UCSC Gene Predictions Based on RefSeq, UniProt, GenBank, and Comparative Genomics
PPP1R1B
PPP1R1B
PPP1R1B
PPP1R1B
Consensus CDS
CCDS11339.1
CCDS11340.1
RefSeq Genes
PPP1R1B/NM_032192
PPP1R1B/NM_181505
Mammalian Gene Collection Full ORF mRNAs
BC001519
Vertebrate Multiz Alignment & PhastCons Conservation (28 Species)
Vertebrate Cons
Chimp
Rhesus
Mouse
Rat
Dog
Cow
Tetraodon
Fugu
rs7212852

rs34257414

Simple Nucleotide Polymorphisms (dbSNP build 128)
rs35797948

Synonymous

Non−synonymous

rs734645

Untranslated

SNPs
Figure 15: Zoomed in view of the 50 and 30 ends of the PPP1R1B gene. Conservation is high inthe exons in the coding region and falls off at the boundaries of exons.

21

Fishing for Genes in the UCSC Browser

search. An MGC clone can be ordered by following links from the Genome Browser to vendors. The MGC Genes track shows the alignment of one full-length MGC clone (BC001519)
for PPP1R1B. As mentioned previously (section
6.3), it is also shown in the Human mRNAs track
since MGC clones are in the GenBank database(Figure 5, Box B).
A click on the alignment for the BC001519
sequence in the MGC Genes track takes theuser to the details page for this MGC transcript(Figure 16). The details page displays a genedescription, the RefSeq accession and RefSeq
description. Additionally, there is information
about the clone, links for downloading protein,mRNA and genomic sequences, the alignment
to the human reference genome sequence, NCBI
clone validation information and links to various
external databases including an MGC clone validation report and links to the MGC website. The
CDS annotation of the MGC clone is frozen, but
the RefSeq transcripts are continually being updated by NCBI manual annotators as more transcript and other experimental evidence becomes
available. The RefSeq CDS similarity table on
the MGC clone details page shows users how
the RefSeq annotations differ to that of the MGC
clone.
To order a clone, the user should follow the
first link in the Links box, Order MGC clone,which directs the user to a portal where clone
distributors are listed. In some cases, there isa direct ordering link to facilitate the ordering
process as seen in Figure 17.

10of this tutorial but there is extensive documentation to help users to navigate use of the Genome
Browser and its integrated tools. To read the
documentation, click on the Help link on the top
blue menu bar found on the Genome Browser
website. Links are also provided on the user interface for each tool. Additionally, questions regarding the website and Genome Browser use
are welcome. Users may search the mailing listarchives (http://genome.ucsc.edu/contacts.html)
and may also send questions via e-mail to themailing list: genome@soe.ucsc.edu.

11

FAQ

Question 1: How do I do a batch search for all
the genes that lie in a specified region of a human chromosome?
Answer 1: The Table Browser is an extremely useful tool for querying the databasetables that underlie the Genome Browser. The
Table Browser can be reached by clicking on
the Tables link on the top blue bar of the UCSC
Genome Bioinformatics web pages. To retrieve
a set of genes from the UCSC Genes set, thesesteps may be followed:

Summary

1. Make sure that the correct assembly is selected. For the hg18 human assembly(NCBI Build 36.1), select Vertebrate as theclade, Human as the genome and Mar.
2006 as the assembly.
2. For the group, select Genes and Gene Prediction Tracks and for the track, select
UCSC Genes.
3. Select knownGene as the table.

The Genome Browser is a very effective tool
for the integration and analysis of biological
data in a genomic context. It provides an easy
method of rapidly locating an MGC clone fora gene of interest with direct links for ordering the clone. Many tools are built into the
Genome Browser; their use is beyond the scope
22

4. Select position. To find genes in a region of the chromosome, type the genomic
location in the text box in the format,
chr1:10000-100000. This example willfind genes on chromosome 1 between base
10,000 and base 100,000. Then press the
lookup button.

Fishing for Genes in the UCSC Browser

Home

Genomes

Genome Browser

Blat

TablesGene Sorter

PCR

SessionFAQ

Help

MGC Clone BC001519.2

Gene
Description

PPP1R1B
Homo sapiens protein phosphatase 1, regulatory (inhibitor) subunit 1B, mRNA (cDNA clone MGC:2855
IMAGE:2987943), complete cds.
RefSeq: NM_181505.2
RefSeq Summary: Midbrain dopaminergic neurons play a critical role in multiple brain functions, and abnormal signaling
through dopaminergic pathways has been implicated in several major neurologic and psychiatric disorders. One well-studied
target for the actions of dopamine is DARPP32. In the densely dopamine- and glutamate-innervated rat caudate-putamen,
DARPP32 is expressed in medium-sized spiny neurons (Ouimet and Greengard, 1990 [PubMed 2191086]) that also
express dopamine D1 receptors (Walaas and Greengard, 1984 [PubMed 6319627]). The function of DARPP32 seems to
be regulated by receptor stimulation. Both dopaminergic and glutamatergic (NMDA) receptor stimulation regulate the extent
of DARPP32 phosphorylation, but in opposite directions (Halpain et al., 1990 [PubMed 2153935]). Dopamine D1
receptor stimulation enhances cAMP formation, resulting in the phosphorylation of DARPP32 (Walaas and Greengard,
1984 [PubMed 6319627]); phosphorylated DARPP32 is a potent protein phosphatase-1 (see MIM 176875) inhibitor(Hemmings et al., 1984 [PubMed 6087160]). NMDA receptor stimulation elevates intracellular calcium, which leads toactivation of calcineurin and dephosphorylation of phospho-DARPP32, thereby reducing the phosphatase-1 inhibitory
activity of DARPP32 (Halpain et al., 1990 [PubMed 2153935]).[supplied by OMIM]. Sequence Note: removed 1 basefrom the 5' end that did not align to the reference genome assembly. Publication Note: This RefSeq record includes a subsetof the publications that are available for this gene. Please see the Entrez Gene record to access additional publications.
Clone Source: Mammalian Gene Collection

MGC Clone Information and Links
Gene

PPP1R1B

Links

Product

protein phosphatase 1, regulatory (inhibitor)

Order MGC clone

Tissuecolon, adenocarcinoma

MGC clone database

Library

NIH_MGC_15

IMAGE clone 2987943

Developmentn/a

Genbank BC001519

CDS

214..720

RefSeq NM_181505.2

Modification date 2008-07-04

Link for ordering
MGC clone

CCDS11340.1
UCSC Gene uc002hsc.1
Brent Lab Clone Validation

RefSeq CDS similarity with MGC clone BC001519
RefSeqPosition

CDS similarity

NM_181505.2 chr17:35038279-35046404 100.00%
NM_032192.2 chr17:35036705-35046403 90.37%

SequencesmRNA

Protein

Genomic

Reference genome mRNA Reference genome protein

Alignments
genomic (browser)

spanmRNA (alignment details) identity aligned

chr17:35038300-35046401 8102 + BC001519:1-1477

100.0% 97.0%

NCBI Clone Validation
mRNA start mRNA end Gene
1481

Notes

1522 PPP1R1B polyA tail: 42 bases do not align to the human genome.

Description and Methods
Click here for details

Figure 16: Details page for the PPP1R1B MGC clone. The details page for the MGC full-length
ORF mRNA (BC001519) shows information about the gene, this MGC clone and its sequence,
similarity between the the RefSeq CDS and the annotated MGC CDS region, alignments, clone
validation information and links to external databases.
23

Fishing for Genes in the UCSC Browser

NCBI » Clone Registry » Order Clones
PubMedNucleotide
Protein
GenomeStructure

PopSetTaxonomy

Go

Search All Databases

Order cDNA clones for Homo sapiens gene PPP1R1B
PPP1R1B: protein phosphatase 1, regulatory (inhibitor) subunit 1B (dopamine and cAMP regulated phosphoprotein,
DARPP-32)
The following clone(s) can be purchased through any of the IMAGE distributors. Some of them have provided direct order link(s) for yourconvenience.

Clone: MGC:2855 (IMAGE:2987943)

Clone
information

I.M.A.G.E. Distributors

Clone Sequence: BC001519.2
Vector: pOTB7
Corresponding RefSeq mRNA: NM_181505.2
from American Type Culture Collection

Press buttons
to order clones

from RZPD German Resource Center for Genome Researchfrom Geneservice Ltd
from Harvard Institute of Proteomics
from Open Biosystems

The I.M.A.G.E Consortium,
headquartered at Lawrence
Livermore National
Laboratory, has handledclone arraying, archiving,and distribution for a numberof large-scale projects,
including MGC and The
ORFeome Collaboration.
I.M.A.G.E Homepage
Distribution of the physicalreagents, either individualclones or entire collections,is handled by the following
U.S. and European
suppliers:
American Type Culture
Collection
Invitrogen,Inc
Open Biosystems
Gene Service,Ltd.
RZPD German Resource
CenterOther clone(s) for the corresponding gene

Mammalian Gene Collection
Figure 17: NCBI page for ordering PPP1R1B cDNA clones. The page
displays links to vendors
The NIH Mammalian Genefor cDNA clones. In this case, there is only one clone listed for this Collection
gene.(MGC)
GenBank
and RefSeq
project
aims to identify at least one
full-ORF
cDNAclone
clone for can be obtained
accessions, and the name of the vector containing the clone are shown.
Theeach human and mouse
gene, produce
a highfrom distributors of Integrated Molecular Analysis of Genomes and their
Expression(I.M.A.G.E)
accuracy sequence, andmake the physical reagents
Consortium clones and links to some of the vendors are provided. easily
Foravailable
thisto clone, direct orderresearchers. The collection
ing links are for American Type Culture Collection (ATCC), RZPD German
Resource
Center foris augmented by alimitednumber of rat cDNAs andGenome Research, Geneservice Ltd., Harvard Institute of Proteomicsnon-mammalianand Open
Biosystems.
clonescoming from the affiliatedZebrafish (ZGC) and
Xenopus (XGC) projects.

5. Finally select the output format. The default will provide the UCSC Gene identifier
and the genomic location for each UCSC
Gene. Press the get output button to perform the search.

MGC Homepage
instructions in the answer
to Question 1, except
ZGC Homepage
XGC Homepage
at step 4, type the nameof the chromosome into
the position box in the format, chr21.

Question 3: How do I do batch retrievals
for full-CDS MGC cDNA clones?
A similar batch search can be done for RefSeq Answer 3: Use the Table Browser. See QuesGenes (table: refGene), Ensembl Genes (table: tion 1 and Question 2 for guidance on batch
ensGene) or other gene set.
retrieval using this tool. To search for full-CDS
MGC cDNA clones, the track to select is MGC
Question 2: How do I do a batch search Genes and the table to select is mgcGenes.
for genes on an entire human chromosome, forexample, chr21?
Answer 2: To carry out this search, follow the24

Fishing for Genes in the UCSC Browser

12

Other resources

URL http://www.genome.org/cgi/content/
abstract/14/4/708.

• UCSC Genome Browser help at http://
genome.ucsc.edu/training• UCSC Genome Browser updates in the
Nucleic Acids Research (NAR) Databaseissues[13, 16, 18, 23]• The original UCSC Genome Browser
publication[21]• UCSC genome browser tutorial[45]• UCSC Genome Browser: Deep support formolecular biomedical research.[28]• Chapter 1, Unit 1.4 of Using Biological
Databases in “Current Protocols in Bioinformatics”• “Genomes, Browsers and Databases: DataMining Tools for Integrated Genomic
Databases”, Peter Schattner (first edition,2008).

References[1] K. G. Becker, K. C. Barnes, T. J.
Bright, and S. A. Wang.
The genetic association database. Nat Genet,
36:431–432, May 2004. ISSN 10614036.
URL http://dx.doi.org/10.1038/
ng0504-431. 10.1038/ng0504-431.
[2] D. A. Benson, I. Karsch-Mizrachi, D. J.
Lipman, J. Ostell, and D. L. Wheeler.
GenBank. Nucl. Acids Res., 36(suppl 1):
D25–30, 2008.
doi: 10.1093/nar/
gkm929. URL http://nar.oxfordjournals.
org/cgi/content/abstract/36/suppl 1/D25.
[3] M. Blanchette, W. J. Kent, C. Riemer,
L. Elnitski, A. F. Smit, K. M. Roskin,
R. Baertsch, K. Rosenbloom, H. Clawson, E. D. Green, D. Haussler, andW. Miller. Aligning Multiple Genomic
Sequences With the Threaded Blockset Aligner. Genome Res., 14(4):708–
715, 2004. doi: 10.1101/gr.1933104.
25[4] Y. Cheng, R. M. Miura, and B. Tian.
Prediction of mRNA polyadenylationsites by support vector machine. Bioinformatics, 22(19):2320–2325, 2006. doi:
10.1093/bioinformatics/btl394.
URL
http://bioinformatics.oxfordjournals.org/
cgi/content/abstract/22/19/2320.
[5] K. Chiu, C.-H. Wong, Q. Chen, P. Ariyaratne, H. Ooi, C.-L. Wei, W.-K. Sung,and Y. Ruan.
Pet-tool: a software
suite for comprehensive processing andmanaging of paired-end ditag (pet) sequence data. BMC Bioinformatics, 7(1):390, 2006. ISSN 1471-2105. doi: 10.
1186/1471-2105-7-390. URL http://www.
biomedcentral.com/1471-2105/7/390.
[6] A. Choo, J. Padmanabhan, A. Chin,
W. J. Fong, and S. K. W. Oh. Immortalized feeders for the scale-up ofhuman embryonic stem cells in feeder
and feeder-free conditions.
Journalof Biotechnology, 122:130–141, Mar2006. URL http://www.sciencedirect.com/
science/article/B6T3C-4HBTDBW-3/1/
b4f66b5f48e5b3227c5916653dbd88f0.
[7] S. J. Cooper, N. D. Trinklein, E. D. Anton, L. Nguyen, and R. M. Myers. Comprehensive analysis of transcriptional promoter structure and function in 1% of thehuman genome. Genome Res., 16(1):
1–10, 2006. doi: 10.1101/gr.4222606.
URL http://genome.cshlp.org/cgi/content/
abstract/16/1/1.
[8] T. A. Down and T. J. P. Hubbard. Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNA. Genome Res., 12(3):458–
461, 2002.
doi: 10.1101/gr.216102.
URL http://www.genome.org/cgi/content/
abstract/12/3/458.

Fishing for Genes in the UCSC Browser

Nucl. Acids Res., 36(suppl 1):D107–113,[9] P. Flicek, B. L. Aken, K. Beal,
2008. doi: 10.1093/nar/gkm967. URL
B. Ballester, M. Caccamo, Y. Chen,
L. Clarke, G. Coates, F. Cunningham,
http://nar.oxfordjournals.org/cgi/content/
abstract/36/suppl 1/D107.
T. Cutts, T. Down, S. C. Dyer, T. Eyre,
S. Fitzgerald, J. Fernandez-Banet, S. Graf,
S. Haider, M. Hammond, R. Holland, [12] A. Grimson, K. K.-H. Farh, W. K. JohnK. L. Howe, K. Howe, N. Johnson,
ston, P. Garrett-Engele, L. P. Lim, and
A. Jenkinson, A. Kahari, D. Keefe,
D. P. Bartel. Microrna targeting specificity
F. Kokocinski, E. Kulesha, D. Lawson,
in mammals: Determinants beyond seed
I. Longden, K. Megy, P. Meidl, B. Overpairing. Molecular Cell, 27:91–105, Julduin, A. Parker, B. Pritchard, A. Prlic,
2007. URL http://www.sciencedirect.com/
S. Rice, D. Rios, M. Schuster, I. Sealy,science/article/B6WSR-4P48CFV-9/1/
G. Slater, D. Smedley, G. Spudich, S. Tre9e1fa34b74d2d78d3ac3fd37b6a4b189.
vanion, A. J. Vilella, J. Vogel, S. White,
M. Wood, E. Birney, T. Cox, V. Curwen, [13] A. S. Hinrichs, D. Karolchik, R. Baertsch,
R. Durbin, X. M. Fernandez-Suarez,
G. P. Barber, G. Bejerano, H. ClawJ. Herrero, T. J. P. Hubbard, A. Kasprzyk,
son, M. Diekhans, T. S. Furey, R. A.
G. Proctor, J. Smith, A. Ureta-Vidal,
Harte, F. Hsu, J. Hillman-Jackson, R. M.
and S. Searle. Ensembl 2008. Nucl.
Kuhn, J. S. Pedersen, A. Pohl, B. J.
Acids
Res.,
36(suppl 1):D707–714,
Raney, K. R. Rosenbloom, A. Siepel,
2008. doi: 10.1093/nar/gkm988. URL
K. E. Smith, C. W. Sugnet, A. Sultanhttp://nar.oxfordjournals.org/cgi/content/
Qurraie, D. J. Thomas, H. Trumbower,
abstract/36/suppl 1/D707.
R. J. Weber, M. Weirauch, A. S. Zweig,
D. Haussler, and W. J. Kent.
The
UCSC Genome Browser Database: up[10] M. Gardiner-Garden and M. Frommer.
Cpg islands in vertebrate
date 2006. Nucl. Acids Res., 34(suppl 1):
D590–598, 2006.
doi: 10.1093/nar/genomes.
Journal of Molecular
gkj144. URL http://nar.oxfordjournals.
Biology,
196:261–282,
Jul 1987.
org/cgi/content/abstract/34/suppl 1/D590.
http://www.sciencedirect.com/
URL
science/article/B6WK7-4DMP8FD-G/1/
f811b0610c688c457165b7da3cdc22b7.
[14] F. Hsu, T. H. Pringle, R. M. Kuhn,
D. Karolchik, M. Diekhans, D. Haussler,
and W. J. Kent. The UCSC Proteome[11] O. L. Griffith, S. B. Montgomery,
Browser. Nucl. Acids Res., 33(suppl 1):
B. Bernier, B. Chu, K. Kasaian, S. Aerts,
D454–458, 2005.
doi: 10.1093/nar/
S. Mahony, M. C. Sleumer, M. Bilenky,gki100. URL http://nar.oxfordjournals.
M. Haeussler, M. Griffith, S. M. Gallo,org/cgi/content/abstract/33/suppl 1/D454.
B. Giardine, B. Hooghe, P. Van Loo,
E. Blanco, A. Ticoll, S. Lithwick,
E. Portales-Casamar, I. J. Donaldson, [15] F. Hsu, W. J. Kent, H. Clawson, R. M.
G. Robertson, C. Wadelius, P. De Bleser,
Kuhn, M. Diekhans, and D. Haussler.
D. Vlieghe, M. S. Halfon, W. WasserThe UCSC Known Genes.
Bioinforman, R. Hardison, C. M. Bergman, S. J.
matics, 22(9):1036–1046, 2006.
doi:
Jones, and T. O. R. A. Consortium.
10.1093/bioinformatics/btl048.
URL
ORegAnno: an open-access communityhttp://bioinformatics.oxfordjournals.org/
driven resource for regulatory annotation.
cgi/content/abstract/22/9/1036.
26

Fishing for Genes in the UCSC Browser[16] D. Karolchik, R. Baertsch, M. Diekhans, [21] W. J. Kent, C. W. Sugnet, T. S. Furey,
T. S. Furey, A. Hinrichs, Y. T. Lu, K. M.
K. M. Roskin, T. H. Pringle, A. M. Zahler,
Roskin, M. Schwartz, C. W. Sugnet,
and D. Haussler. The Human Genome
D. J. Thomas, R. J. Weber, D. Haussler,
Browser at UCSC. Genome Res., 12(6):and W. J. Kent. The UCSC Genome
996–1006, 2002. doi: 10.1101/gr.229102.
Browser Database.
Nucl. Acids Res.,
URL http://genome.cshlp.org/cgi/content/
31(1):51–54, 2003. doi: 10.1093/nar/
abstract/12/6/996.
gkg129. URL http://nar.oxfordjournals.
[22] W. J. Kent, R. Baertsch, A. Hinrichs,
org/cgi/content/abstract/31/1/51.
W. Miller, and D. Haussler.
Evolution’s cauldron: Duplication, deletion,[17] D. Karolchik, A. S. Hinrichs, T. S.
and rearrangement in the mouse and huFurey, K. M. Roskin, C. W. Sugman genomes. Proceedings of the Nanet, D. Haussler, and W. J. Kent.
tional Academy of Sciences of the United
The UCSC Table Browser data retrieval
States of America, 100(20):11484–11489,
tool.
Nucl. Acids Res., 32(suppl 1):
2003. doi: 10.1073/pnas.1932072100.
D493–496, 2004.
doi: 10.1093/nar/
URL http://www.pnas.org/content/100/20/
gkh103. URL http://nar.oxfordjournals.
11484.abstract.
org/cgi/content/abstract/32/suppl 1/D493.
[18] D. Karolchik, R. M. Kuhn, R. Baertsch,G. P. Barber, H. Clawson, M. Diekhans,
B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller,
J. S. Pedersen, A. Pohl, B. J. Raney,
B. Rhead, K. R. Rosenbloom, K. E.
Smith, M. Stanke, A. Thakkapallayil,
H. Trumbower, T. Wang, A. S. Zweig,
D. Haussler, and W. J. Kent. The UCSC
Genome Browser Database: 2008 update.
Nucl. Acids Res., 36(suppl 1):
D773–779, 2008.
doi: 10.1093/nar/
gkm966. URL http://nar.oxfordjournals.
org/cgi/content/abstract/36/suppl 1/D773.
[19] W. Kent, F. Hsu, D. Karolchik, R. M.
Kuhn, H. Clawson, H. Trumbower, and
D. Haussler. Exploring relationships andmining data with the UCSC Gene Sorter.
Genome Res., 15(5):737–741, 2005. doi:
10.1101/gr.3694705. URL http://www.
genome.org/cgi/content/abstract/15/5/737.
[20] W. J. Kent. BLAT: The BLAST-like alignment tool. Genome Res, 12:656–664,
2002.

[23] R. M. Kuhn, D. Karolchik, A. S. Zweig,
H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke,
K. E. Smith, A. Siepel, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl,
J. S. Pedersen, F. Hsu, A. S. Hinrichs,
R. A. Harte, M. Diekhans, H. Clawson,
G. Bejerano, G. P. Barber, R. Baertsch,
D. Haussler, and W. J. Kent.
The
UCSC genome browser database: update
2007.
Nucl. Acids Res., 35(suppl 1):
D668–673, 2007.
doi: 10.1093/nar/
gkl928. URL http://nar.oxfordjournals.
org/cgi/content/abstract/35/suppl 1/D668.
[24] J. Y. Lee, I. Yeh, J. Y. Park, and B. Tian.
PolyA DB 2:
mRNA polyadenylation sites in vertebrate genes.
Nucl.
Acids
Res.,
35(suppl 1):D165–168,
2007. doi: 10.1093/nar/gkl870. URL
http://nar.oxfordjournals.org/cgi/content/
abstract/35/suppl 1/D165.
[25] B. P. Lewis, I.-h. Shih, M. W. JonesRhoades, D. P. Bartel, and C. B. Burge.
Prediction of mammalian microrna targets.
Cell, 115:787–798, Dec 2003.

27

Fishing for Genes in the UCSC Browser

URL
http://www.sciencedirect.com/
science/article/B6WSN-4C5RJXX-4/1/
daacc44b2dc4cbd20152154f2556cbfb.

hab, A. Ridwan, C. H. Wong, E. T. Liu,and Y. Ruan. Gene identification signature(gis) analysis for transcriptome characterization and genome annotation. Nat Meth,
2:105–111, Feb 2005. ISSN 1548-7091.
URL http://dx.doi.org/10.1038/nmeth733.
10.1038/nmeth733.

[26] B. P. Lewis, C. B. Burge, and D. P.
Bartel. Conserved seed pairing, often
flanked by adenosines, indicates thatthousands of human genes are microrna
targets.
Cell, 120:15–20, Jan 2005. [31] K. D. Pruitt, T. Tatusova, and D. R. MaURL
http://www.sciencedirect.com/
glott. NCBI reference sequences (Refscience/article/B6WSN-4F7PRGS-6/1/
Seq): a curated non-redundant sequence
4caeed2c84a218c0bd80bdf7fe1506c4.
database of genomes, transcripts and proteins.
Nucl. Acids Res., 35(suppl 1):[27] J. Majewski and J. Ott. Distribution and
D61–65, 2007.
doi: 10.1093/nar/
Characterization of Regulatory Elements
gkl842.
URL
http://nar.oxfordjournals.
in the Human Genome. Genome Res., 12
org/cgi/content/abstract/35/suppl 1/D61.
(12):1827–1836, 2002. doi: 10.1101/gr.
606402.

[32] S. Schwartz, W. J. Kent, A. Smit,
Z. Zhang, R. Baertsch, R. C. Hardison,
D. Haussler, and W. Miller. Human-Mouse
Alignments with BLASTZ. Genome Res.,
13(1):103–107, 2003. doi: 10.1101/gr.
809403. URL http://www.genome.org/cgi/
content/abstract/13/1/103.

[28] M. E. Mangan, J. M. Williams, S. M.
Lathe, D. Karolchik, and W. C. Lathe III.
Biotechnology Annual Review, volume
Volume 14, chapter UCSC Genome
Browser: Deep support for molecularbiomedical research, pages 63–108. Elsevier, 2008. URL http://www.sciencedirect.
com/science/article/B7CTS-4SX89K0-8/ [33] S. T. Sherry, M.-H. Ward, M. Kholodov,
J. Baker, L. Phan, E. M. Smigielski, and2/fd8ba712b4824e759a88e34dac02e743.
K. Sirotkin. dbSNP: the NCBI databaseof genetic variation. Nucl. Acids Res., 29[29] W. Miller, K. Rosenbloom, R. C. Hardi(1):308–311, 2001. doi: 10.1093/nar/29.
son, M. Hou, J. Taylor, B. Raney,
1.308. URL http://nar.oxfordjournals.org/
R. Burhans, D. C. King, R. Baertsch,
cgi/content/abstract/29/1/308.
D. Blankenberg, S. L. Kosakovsky Pond,
A. Nekrutenko, B. Giardine, R. S. Harris, S. Tyekucheva, M. Diekhans, T. H. [34] A. Siepel, G. Bejerano, J. S. Pedersen,
A. S. Hinrichs, M. Hou, K. Rosenbloom,
Pringle, W. J. Murphy, A. Lesk, G. M.
H. Clawson, J. Spieth, L. W. Hillier,Weinstock, K. Lindblad-Toh, R. A. Gibbs,
S. Richards, G. M. Weinstock, R. K. WilE. S. Lander, A. Siepel, D. Haussler, andson, R. A. Gibbs, W. J. Kent, W. Miller,
W. J. Kent. 28-Way vertebrate alignand D. Haussler. Evolutionarily conserved
ment and conservation track in the UCSC
elements in vertebrate, insect, worm, andGenome Browser.
Genome Res., 17
yeast genomes. Genome research, 15(8):(12):1797–1808, 2007. doi: 10.1101/gr.
1034–1040, 2005.
6761107. URL http://www.genome.org/
cgi/content/abstract/17/12/1797.
[35] A. Siepel, M. Diekhans, B. Brejova,[30] P. Ng, C.-L. Wei, W.-K. Sung, K. P. Chiu,
L. Langton, M. Stevens, C. L. Comstock,
L. Lipovich, C. C. Ang, S. Gupta, A. ShaC. Davis, B. Ewing, S. Oommen, C. Lau,
28

Fishing for Genes in the UCSC Browser

H.-C. Yu, J. Li, B. A. Roe, P. Green,
D. S. Gerhard, G. Temple, D. Haussler,
and M. R. Brent. Targeted discovery
of novel human exons by comparative
genomics. Genome Res., 17(12):1763–
1773, 2007. doi: 10.1101/gr.7128207.
URL http://www.genome.org/cgi/content/
abstract/17/12/1763.

Kuznetsov, W.-K. Sung, L. D. Miller,
B. Lim, E. T. Liu, Q. Yu, H.-H. Ng,
and Y. Ruan. A global map of p53
transcription-factor binding sites in thehuman genome. Cell, 124:207–219, Jan2006. URL http://www.sciencedirect.com/
science/article/B6WSN-4J1B5X8-S/1/
199bb4dbe7ad1d5297fe65359c6dabec.

[36] M. Stanke, M. Diekhans, R. Baertsch, [41] L. G. Wilming, J. G. R. Gilbert, K. Howe,S. Trevanion, T. Hubbard, and J. L.
and D. Haussler. Using native and synHarrow.
The vertebrate genome
tenically mapped cDNA alignments toannotation (Vega) database.
Nucl.
improve de novo gene finding. BioinAcidsRes.,
36(suppl
1):D753–760,
formatics, page btn013, 2008.
doi:
2008. doi: 10.1093/nar/gkm987. URL
10.1093/bioinformatics/btn013.
URL
http://nar.oxfordjournals.org/cgi/content/
http://bioinformatics.oxfordjournals.org/
abstract/36/suppl 1/D753.
cgi/content/abstract/btn013v1.
[37] T. M. P. Team. The Status, Quality, and [42] G. W. Yeo, E. Van Nostrand, D. Holste,
T. Poggio, and C. B. Burge. Identification
Expansion of the NIH Full-Length cDNAand analysis of alternative splicing events
Project: The Mammalian Gene Collecconserved in human and mouse. Protion (MGC). Genome Res., 14(10b):2121–
ceedings of the National Academy of Sci2127, 2004. doi: 10.1101/gr.2596504.
ences of the United States of America, 102
URL http://www.genome.org/cgi/content/(8):2850–2855, 2005. doi: 10.1073/pnas.
abstract/14/10b/2121.
0409742102. URL http://www.pnas.org/[38] D. J. Thomas, H. Trumbower, A. D. Kern,content/102/8/2850.abstract.
B. L. Rhead, R. M. Kuhn, D. Haussler,
and W. J. Kent. Variation resources at UC [43] K. I. Zeller, X. Zhao, C. W. H. Lee,K. P. Chiu, F. Yao, J. T. Yustein, H. S.
Santa Cruz. Nucl. Acids Res., 35(suppl 1):
Ooi, Y. L. Orlov, A. Shahab, H. C. Yong,D716–720, 2007.
doi: 10.1093/nar/Y. Fu, Z. Weng, V. A. Kuznetsov, W.gkl953. URL http://nar.oxfordjournals.
K. Sung, Y. Ruan, C. V. Dang, andorg/cgi/content/abstract/35/suppl 1/D716.
C.-L. Wei. Global mapping of c-Myc[39] N. D. Trinklein, S. F. Aldred, S. J. Hartbinding sites and target gene networks
man, D. I. Schroeder, R. P. Otillar, andin human B cells. Proceedings of theR. M. Myers. An Abundance of BidirecNational Academy of Sciences, 103(47):tional Promoters in the Human Genome.
17834–17839, 2006. doi: 10.1073/pnas.
Genome Res., 14(1):62–66, 2004. doi:
0604129103. URL http://www.pnas.org/
10.1101/gr.1982804. URL http://genome.
content/103/47/17834.abstract.
cshlp.org/cgi/content/abstract/14/1/62.
[44] J. Zhu, J. Z. Sanborn, M. Diekhans, C. B.
[40] C.-L. Wei, Q. Wu, V. B. Vega, K. P.
Lowe, T. H. Pringle, and D. Haussler.
Chiu, P. Ng, T. Zhang, A. Shahab, H. C.
Comparative genomics search for losses of
Yong, Y. Fu, Z. Weng, J. Liu, X. D.
long-established genes on the human linZhao, J.-L. Chew, Y. L. Lee, V. A.
eage. PLoS Computational Biology, 3:29Fishing for Genes in the UCSC Browser

e247 EP –, Dec 2007. URL http://dx.doi.
org/10.1371/journal.pcbi.0030247.
[45] A. S. Zweig, D. Karolchik, R. M.
Kuhn, D. Haussler, and W. J.
Kent.
Ucsc genome browser tutorial. Genomics, 92:75–84, Aug 2008.
URL
http://www.sciencedirect.com/
science/article/B6WG1-4SN8V4K-1/2/
52fefdb7d8345ae05aa0ec653a0adc27.

30