Housekeeping gene

Housekeeping gene
In molecular biology, housekeeping genes are typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions. Although some housekeeping genes are expressed at relatively constant rates in most non-pathological situations, the expression of other housekeeping genes may vary depending on experimental conditions.
The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA. For experimental purposes, the expression of one or multiple housekeeping genes is used as a reference point for the analysis of expression levels of other genes. The key criterion for the use of a housekeeping gene in this manner is that the chosen housekeeping gene is uniformly expressed with low variance under both control and experimental conditions. Validation of housekeeping genes should be performed before their use in gene expression experiments such as RT-PCR. Recently a web-based database of human and mouse housekeeping genes and reference genes/transcripts, named Housekeeping and Reference Transcript Atlas (HRT Atlas), was developed to offer updated list of housekeeping genes and reliable candidate reference genes/transcripts for RT-qPCR data normalization. This database can be accessed at http://www.housekeeping.unicamp.br.
Housekeeping gene regulation
Housekeeping genes account for majority of the active genes in the genome, and their expression is obviously vital to survival. The housekeeping gene expression levels are fine-tuned to meet the metabolic requirements in various tissues. Biochemical studies on transcription initiation of the housekeeping gene promoters have been difficult, partly due to the less-characterized promoter motifs and transcription initiation process.
Human housekeeping gene promoters are generally depleted of TATA-box, have high GC content and high incidence of CpG Islands. In Drosophila, where promoter specific CpG Islands are absent, housekeeping gene promoters contain DNA elements like DRE, E-box or DPE. Transcription start sites of housekeeping genes can span over a region of around 100 bp whereas transcription start sites of developmentally regulated genes are usually focused in a narrow region. Little is known about how the dispersed transcription initiation of housekeeping gene is established. There are transcription factors that are specifically enriched on and regulate housekeeping gene promoters. Furthermore, housekeeping promoters are regulated by housekeeping enhancers but not developmentally regulated enhancers.
Common housekeeping genes in humans
The following is a partial list of "housekeeping genes." For a more complete and updated list, see HRT Atlas database compiled by Bidossessi W. Hounkpe et al. The database was constructed by mining more than 12000 human and mouse RNA-seq datasets.
Gene expression
Transcription factors
ATF1 NM_005171
ATF2 NM_001880
ATF4 Activating transcription factor 4 NM_001675
ATF6 NM_007348
ATF7 NM_001206682
ATF7IP NM_018179
BTF3 NM_001207 Homo sapiens basic transcription factor 3
E2F4 Homo sapiens E2F transcription factor 4, p107/p130-binding (E2F4), mRNA
ERH (gene) Enhancer of rudimentary homolog of drosophila (which in turn is the first enzymatic step in pyrimidine synthesis. Regulated by MITF)
HMGB1 High mobility group box binds DNA
ILF2 Homo sapiens interleukin enhancer binding factor 2, 45kDa (ILF2), mRNA
IER2 formerly ETR101 Immediate Early Protein?
JUND Homo sapiens jun D proto-oncogene (JUND), mRNA
TCEB2 Elongin Matheo er rar
Repressors
PUF60 Homo sapiens fuse-binding protein-interacting repressor (SIAHBP1), transcript
RNA splicing
BAT1 aka DDX39B
HNRPD Homo sapiens heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA
HNRPK Homo sapiens heterogeneous nuclear ribonucleoprotein K (HNRPK), transcript
PABPN1 poly(A) binding protein, nuclear 1
SRSF3 splicing factor, arginine/serine-rich
Translation factors
EIF1 aka SUI1
EIF1AD
EIF1B
EIF2A
EIF2AK1
EIF2AK3
EIF2AK4
EIF2AK1
EIF2B2
EIF2B3
EIF2B4
EIF2S2
EIF3A
EIF3B
EIF3D formerly EIF3S4
EIF3G
EIF3I
EIF3H
EIF3J
EIF3K
EIF3L
EIF3M
EIF3S5
EIF3S8
EIF4A1
EIF4A2
EIF4A3
EIF4E2
EIF4G1
EIF4G2
EIF4G3
EIF4H
EIF5
EIF5
EIF5A
EIF5AL1
EIF5B
EIF6
TUFM Tu translational elongation factor mitochondrial
tRNA synthesis
AARS NM_001605 alanyl-tRNA synthetase
AARS2 NM_020745 alanyl-tRNA synthetase 2, mitochondrial
AARSD1 NM_001261434 alanyl-tRNA synthetase domain containing 1
CARS NM_001751 cysteinyl-tRNA synthetase
CARS2 NM_024537 cysteinyl-tRNA synthetase 2, mitochondrial (putative)
DARS NM_001349 aspartyl-tRNA synthetase
DARS2 NM_018122 aspartyl-tRNA synthetase 2, mitochondrial
EARS2 NM_001083614 glutamyl-tRNA synthetase 2, mitochondrial
FARS2 NM_006567 phenylalanyl-tRNA synthetase 2, mitochondrial
FARSA NM_004461 phenylalanyl-tRNA synthetase, alpha subunit
FARSB NM_005687 phenylalanyl-tRNA synthetase, beta subunit
GARS NM_002047 glycyl-tRNA synthetase
HARS NM_002109 histidyl-tRNA synthetase
HARS2 NM_012208 histidyl-tRNA synthetase 2, mitochondrial
IARS NM_002161 isoleucyl-tRNA synthetase
IARS2 NM_018060 isoleucyl-tRNA synthetase 2, mitochondrial
KARS NM_005548 Homo sapiens lysyl-tRNA synthetase (KARS), mRNA
LARS2 NM_015340 isoleucyl-tRNA synthetase 2, mitochondrial
MARS NM_004990 methionyl-tRNA synthetase
MARS2 NM_138395 methionyl-tRNA synthetase 2, mitochondrial
NARS NM_004539 asparaginyl-tRNA synthetase
NARS2 NM_024678 asparaginyl-tRNA synthetase 2, mitochondrial (putative)
QARS NM_005051 glutaminyl-tRNA synthetase
RARS NM_002884 arginyl-tRNA synthetase
RARS2 NM_020320 arginyl-tRNA synthetase 2, mitochondrial
SARS NM_006513 Homo sapiens seryl-tRNA synthetase (SARS), mRNA
TARS NM_152295 threonyl-tRNA synthetase
VARS2 NM_020442 valyl-tRNA synthetase 2, mitochondrial
WARS2 NM_015836 tryptophanyl tRNA synthetase 2, mitochondrial
YARS NM_003680 Homo sapiens tyrosyl-tRNA synthetase (YARS), mRNA
YARS2 NM_001040436 Homo sapiens tyrosyl-tRNA synthetase (YARS), mRNA mitochondrial
RNA binding protein
ELAVL1
Ribosomal proteins
RPL5
RPL8
RPL9
RPL10A
RPL11
RPL14
RPL25
RPL26L1
RPL27
RPL30
RPL32
RPL34
RPL35
RPL35A
RPL36AL
RPS5
RPS6
RPS6KA3
RPS6KB1
RPS6KB2
RPS13
RPS19BP1
RPS20
RPS23
RPS24
RPS27 transcribed with ubiquitin (see FAU (gene))
RPN1 Ribophorin anchors the ribosome to rough endoplasmic reticulum
Mitochondrial ribosomal proteins
MRPL9
MRPL1
MRPL10
MRPL11
MRPL12
MRPL13
MRPL14
MRPL15
MRPL16
MRPL17
MRPL18
MRPL19
MRPL2
MRPL20
MRPL21
MRPL22
MRPL23
MRPL24
MRPL27
MRPL28
MRPL3
MRPL30
MRPL32
MRPL33
MRPL35
MRPL36
MRPL37
MRPL38
MRPL4
MRPL40
MRPL41
MRPL42
MRPL43
MRPL44
MRPL45
MRPL46
MRPL47
MRPL48
MRPL49
MRPL50
MRPL51
MRPL52
MRPL53
MRPL54
MRPL55
MRPL9
MRPS10
MRPS11
MRPS12
MRPS14
MRPS15
MRPS16
MRPS17
MRPS18A
MRPS18B
MRPS18C
MRPS2
MRPS21
MRPS22
MRPS23
MRPS24
MRPS25
MRPS26
MRPS27
MRPS28
MRPS30
MRPS31
MRPS33
MRPS34
MRPS35
MRPS5
MRPS6
MRPS7
MRPS9
RNA polymerase
POLR1C
POLR1D
POLR1E
POLR2A
POLR2B
POLR2C
POLR2D
POLR2E
POLR2F
POLR2G
POLR2H
POLR2I
POLR2J
POLR2K
POLR2L
POLR3C
POLR3E
POLR3GL
POLR3K
Protein processing
PPID Peptidyl-prolyl cis-trans isomerase D
PPIE Peptidyl-prolyl cis-trans isomerase E
PPIF Peptidyl-prolyl cis-trans isomerase F
PPIG Peptidyl-prolyl cis-trans isomerase G
PPIH Cyclophilin H
CANX Calnexin. Folding of glycoproteins within endoplasmic reticulum
CAPN1 Calpain subunit
CAPN7
CAPNS1 Calpain protease subunit
NACA Nascent polypeptide associated complex alpha polypeptide
NACA2
PFDN2 Prefoldin 2
PFDN4 Prefoldin 4
PFDN5 Prefoldin 5
PFDN6 Prefoldin 6
SNX2 Sorting nexin 2
SNX3 Sorting nexin 3
SNX4 Sorting nexin 4
SNX5 Sorting nexin 5
SNX6 Sorting nexin 6
SNX9 Sorting nexin 9
SNX12 Sorting nexin 12
SNX13 Sorting nexin 13
SNX17 Sorting nexin 17
SNX18 Sorting nexin 18
SNX19 Sorting nexin 19
SNX25 Sorting nexin 25
SSR1 Translocon-associated protein TRAPA. Protein translocation in ER
SSR2 Translocon-associated protein TRAPB. Protein translocation in ER
SSR3 Translocon-associated protein TRAPG. Protein translocation in ER
SUMO1 Protein targeting
SUMO3 Protein targeting
Heat shock proteins
HSPA4
HSPA5
HSPA8
HSPA9
HSPA14
HSBP1
Histone
HIST1H2BC
H1FX
H2AFV
H2AFX
H2AFY Histone 2 Subfamily
H2AFZ essential for embryogenesis
Cell cycle
There is significant overlap in function with regards to some of these proteins. In particular, the Rho-related genes are important in nuclear trafficking (i.e.: mitosis) as well as with mobility along the cytoskeleton in general. These genes of particular interest in cancer research.
ARHGAP35
ARHGAP5
ARHGDIA
ARHGEF10L Rho guanine nucleotide exchange factor 10L
ARHGEF11 Rho guanine nucleotide exchange factor 11
ARHGEF40 Rho guanine nucleotide exchange factor 40
ARHGEF7 Rho guanine nucleotide exchange factor 7
RAB10 NM_016131 The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes
RAB11A NM_004663
RAB11B NM_004218
RAB14 NM_016322
RAB18 NM_021252
RAB1A NM_004161 Homo sapiens RAB1A, member RAS oncogene family (RAB1A), mRNA
RAB1B NM_030981
RAB21 NM_014999
RAB22A NM_020673
RAB2A NM_002858
RAB2B NM_001163380
RAB3GAP1 NM_012233
RAB3GAP2 NM_012414
RAB40C NM_021168
RAB4A NM_004578
RAB5A NM_004162
RAB5B NM_002865
RAB5C NM_004583
RAB6A NM_002868
RAB7A NM_004637
RAB9A NM_004251
RABEP1 NM_004703
RABEPK NM_005833
RABGEF1 NM_014504
RABGGTA NM_004581
RABGGTB NM_004582
CENPB Centromere protein B
CTBP1 Centromere protein T
CCNB1IP1 NM_021178 E3 ubiquitin-protein ligase. Modulates cyclin B levels and participates in the regulation of cell cycle progression through the G2 phase
CCNDBP1 NM_012142 May negatively regulate cell cycle progression
CCNG1 NM_004060 May play a role in growth regulation
CCNH NM_001239 Involved in cell cycle control and in RNA transcription by RNA polymerase II. Its expression and activity are constant throughout the cell cycle
CCNK NM_001099402 Regulatory subunit of cyclin-dependent kinases that mediates phosphorylation of the large subunit of RNA polymerase II
CCNL1 NM_020307 Transcriptional regulator which participates in regulating the pre-mRNA splicing process
CCNL2 NM_030937 Transcriptional regulator which participates in regulating the pre-mRNA splicing process. Also modulates the expression of critical apoptotic factor, leading to cell apoptosis.
CCNY NM_145012 Positive regulatory subunit of the cyclin-dependent kinases CDK14/PFTK1 and CDK16. Acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase
PPP1CA NM_002708 Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets
PPP1CC NM_002710
PPP1R10 NM_002714
PPP1R11 NM_021959 Homo sapiens protein phosphatase 1, regulatory (inhibitor) subunit 11 (PPP1R11),
PPP1R15B NM_032833
PPP1R37 NM_019121
PPP1R7 NM_002712
PPP1R8 NM_002713
PPP2CA NM_002715
PPP2CB NM_001009552
PPP2R1A NM_014225 Negative regulator of growth and cell divisionHomo sapiens protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65),
PPP2R2A NM_002717
PPP2R2D NM_018461
PPP2R3C NM_017917
PPP2R4 NM_021131
PPP2R5A NM_006243
PPP2R5B NM_006244
PPP2R5C NM_002719
PPP2R5D NM_006245
PPP2R5E NM_006246
PPP4C NM_002720
PPP4R1 NM_005134
PPP4R2 NM_174907
PPP5C NM_006247
PPP6C NM_002721
PPP6R2 NM_014678
PPP6R3 NM_018312
RAD1Homo sapiens ribonuclease/angiogenin inhibitor (RNH), mRNA
RAD17 NM_002869 Essential for sustained cell growth, maintenance of chromosomal stability, and ATR-dependent checkpoint activation upon DNA damage
RAD23B NM_002873
RAD50 NM_005732
RAD51C NM_002874
IST1 (locates to central dividing line of dividing cells)
Apoptosis
DAD1 Defender against cell death
DAP3 Involved in mediating interferon-gamma-induced cell death.
DAXX Death Associated Protein 6
Oncogenes
ARAF
MAZ (gene)
MYC also considered a transcription factor
DNA repair/replication
MCM3AP possibly a primase
XRCC5 NM_021141 Ku80
XRCC6 NM_001469 Homo sapiens thyroid autoantigen: Single-stranded DNA-dependent ATP-dependent helicase. Has a role in chromosome translocation.
Metabolism
PRKAG1 Senses energy level and inactivates HMGCoA reductase and Acetyl CoA Carboxylase
PRKAA1 NM_006251 Catalytic subunit of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism
PRKAB1 NM_006253 Non-catalytic subunit of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism
PRKACA NM_002730 Phosphorylates a large number of substrates in the cytoplasm and the nucleus.
PRKAG1 NM_002733 Homo sapiens protein kinase, AMP-activated, gamma 1 non-catalytic subunit (PRKAG1), mRNA
PRKAR1A NM_002734 Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells
PRKRIP1 NM_024653 Binds double-stranded RNA. Inhibits EIF2AK2 kinase activity (By similarity).
Carbohydrate metabolism
ALDOA
B3GALT6 NM_080605
B4GALT3 NM_003779 Homo sapiens UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3
B4GALT5 NM_004776
B4GALT7 NM_007255
GSK3A
GSK3B
TPI1
PGK1 Phosphoglycerate kinase
PGAM5
ENOPH1 Enolase phosphatase
LDHA Lactate dehydrogenase
TALDO1 Transaldolase in pentose shunt
TSTA3 Mannose metabolism
Citric Acid Cycle
SDHA NM_004168 Succinate Dehydrogenase subunit A
SDHAF2 NM_017841
SDHB NM_002973 Iron-sulfur protein (IP) subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q)
SDHC NM_003000 Membrane-anchoring subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q).
SDHD NM_003001
Lipid metabolism
HADHA Trifunctional protein subunit alpha
Amino acid metabolism
COMT Catechol-O-methyl transferase)
NADH dehydrogenase
NDUFA2NM_002488
NDUFA3 NM_004542
NDUFA4 NM_002489
NDUFA5 NM_005000
NDUFA6 NM_002490
NDUFA7 NM_005001 Homo sapiens NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa
NDUFA8 NM_014222
NDUFA9 NM_005002
NDUFA10 NM_004544
NDUFA11 NM_175614
NDUFA12 NM_018838
NDUFA13 NM_015965
NDUFAF2 NM_174889
NDUFAF3 NM_199069
NDUFAF4 NM_014165
NDUFB2 NM_004546
NDUFB3 NM_002491
NDUFB4 NM_004547
NDUFB5 NM_002492
NDUFB6 NM_002493
NDUFB7 NM_004146 Homo sapiens NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa
NDUFB10 NM_004548
NDUFB11 NM_019056
NDUFB8 NM_005004
NDUFB9 NM_005005
NDUFC1 NM_002494Homo sapiens NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1, 6kDa
NDUFC2 NM_004549
NDUFC2-KCTD14 NM_001203260
NDUFS5
NDUFV2
NDUFS2 NM_004550
NDUFS3 NM_004551
NDUFS4 NM_002495
NDUFS5 NM_004552 Homo sapiens NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa
NDUFS6 NM_004553
NDUFS7 NM_024407
NDUFS8 NM_002496
NDUFV1 NM_007103 Homo sapiens NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa (NDUFV1),
NDUFV2 NM_021074 Homo sapiens NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa (NDUFV2),
Cytochrome C oxidase
(Note that COX1, COX2, and COX3 are mitochondrially encoded)
COX4I1 001861
COX5B NM_001862
COX6B1 NM_001863
COX6C NM_004374
COX7A2 NM_001865 Homo sapiens cytochrome c oxidase subunit VIIa polypeptide 2 (liver) (COX7A2),
COX7A2L NM_004718
COX7C NM_001867
COX8
COX8A NM_004074 Homo sapiens cytochrome c oxidase subunit VIII (COX8), nuclear gene encoding
COX11 NM_004375
COX14 NM_032901
COX15 NM_004376
COX16 NM_016468
COX19 NM_001031617
COX20 NM_198076
CYC1 Homo sapiens cytochrome c-1 (CYC1)
UQCC NM_018244 Required for the assembly of the ubiquinol-cytochrome c reductase complex (mitochondrial respiratory chain complex III or cytochrome b-c1 complex)
UQCR10 NM_013387
UQCR11 NM_006830 Homo sapiens ubiquinol-cytochrome c reductase (6.4kD) subunit (UQCR), mRNA
UQCRB NM_006294
UQCRC1 NM_003365 Homo sapiens ubiquinol-cytochrome c reductase core protein I (UQCRC1), mRNA
UQCRC2 NM_003366
UQCRHL NM_001089591
UQCRQ NM_014402 Homo sapiens low molecular mass ubiquinone-binding protein (9.5kD) (QP-C), mRNA
ATPase
ATP2C1 NM_014382
ATP5A1 NM_004046 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, alpha
ATP5B NM_001686
ATP5C1 NM_005174
ATP5D NM_001687 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta
ATP5F1 NM_001688
ATP5G2 NM_005176
ATP5G3 NM_001689 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c
ATP5H NM_006356 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d
ATP5J NM_001685
ATP5J2 NM_004889 Homo sapiens ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f,
ATP5J2-PTCD1 NM_001198879
ATP5L NM_006476
ATP5O NM_001697 Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit
ATP5S NM_015684
ATP5SL NM_018035
ATP6AP1 NM_001183 Homo sapiens ATPase, H+ transporting, lysosomal interacting protein 1 (ATP6IP1),
ATP6V0A2 NM_012463
ATP6V0B NM_004047 Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c (ATP6V0B),
ATP6V0C NM_001694 Homo sapiens ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c (ATP6V0C),
ATP6V0D1 NM_004691
ATP6V0E1 NM_003945
ATP6V1C1 NM_001695
ATP6V1D NM_015994
ATP6V1E1 NM_001696 Homo sapiens ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E isoform 1
ATP6V1F NM_004231 Homo sapiens ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F (ATP6V1F),
ATP6V1G1 NM_004888 Homo sapiens ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 1
ATP6V1H NM_015941
ATPAF2 NM_145691
ATPIF1 NM_016311
Lysosome
CTSD can degrade insulin in hepatocytes
CSTB May protect cell from leaking lysosomes
LAMP1
LAMP2
M6PR
Proteasome
PSMA1 NM_002786
PSMA2 NM_002787
PSMA3 NM_002788
PSMA4 NM_002789
PSMA5 NM_002790
PSMA6 NM_002791
PSMA7 NM_002792 Homo sapiens proteasome (prosome, macropain) subunit, alpha type, 7 (PSMA7),
PSMB1 NM_002793 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 1 (PSMB1), mRNA
PSMB2 NM_002794 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 2 (PSMB2), mRNA
PSMB3 NM_002795
PSMB4 NM_002796 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 4 (PSMB4), mRNA
PSMB5 NM_002797
PSMB6 NM_002798
PSMB7 NM_002799 Homo sapiens proteasome (prosome, macropain) subunit, beta type, 7 (PSMB7), mRNA
PSMC2 NM_002803
PSMC3 NM_002804
PSMC4 NM_006503
PSMC5 NM_002805
PSMC6 NM_002806
PSMD1 NM_002807
PSMD10 NM_002814
PSMD11 NM_002815 Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 11
PSMD12 NM_002816
PSMD13 NM_002817
PSMD14 NM_005805
PSMD2 NM_002808
PSMD3 NM_002809
PSMD4 NM_002810
PSMD5 NM_005047
PSMD6 NM_014814
PSMD7 NM_002811
PSMD8 NM_002812 Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 (PSMD8),
PSMD9 NM_002813
PSME2 NM_002818 Homo sapiens proteasome (prosome, macropain) activator subunit 2 (PA28 beta)
PSME3 NM_005789
PSMF1 NM_006814
PSMG2 NM_020232
PSMG3 NM_032302
PSMG4 NM_001128591
UBA1 NM_003334 Homo sapiens ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature
UBA2 NM_005499
UBA3 NM_003968
UBA5 NM_024818
UBA52 NM_003333
UBAC2 NM_177967
UBALD1 NM_145253
UBAP1 NM_016525
UBAP2L NM_014847
UBB NM_018955 Homo sapiens ubiquitin B (UBB), mRNA
UBC NM_021009 Homo sapiens ubiquitin C (UBC), mRNA
UBE2A NM_003336
UBE2B NM_003337
UBE2D2 NM_003339 Homo sapiens ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
UBE2D3 NM_003340
UBE2D4 NM_015983
UBE2E1 NM_003341
UBE2E2 NM_152653
UBE2E3 NM_006357
UBE2F NM_080678
UBE2G2 NM_003343
UBE2H NM_003344
UBE2I NM_003345 Homo sapiens ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast) (UBE2I),
UBE2J1 NM_016021
UBE2J2 NM_058167
UBE2K NM_005339
UBE2L3 NM_003347
UBE2M NM_003969 Homo sapiens ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast) (UBE2M),
UBE2N NM_003348
UBE2NL NM_001012989
UBE2Q1 NM_017582
UBE2R2 NM_017811
UBE2V1 NM_021988
UBE2V2 NM_003350
UBE2W NM_018299
UBE2Z NM_023079
UBE3A NM_000462
UBE3B NM_130466
UBE3C NM_014671
UBE4A NM_004788
UBE4B NM_006048
USP10 NM_005153
USP14 NM_005151
USP16 NM_006447
USP19 NM_006677
USP22 NM_015276
USP25 NM_013396
USP27X NM_001145073
USP33 NM_015017
USP38 NM_032557
USP39 NM_006590
USP4 NM_003363
USP47 NM_017944
USP5 NM_003481
USP7 NM_003470
USP8 NM_005154
USP9X NM_001039590
Ribonuclease
RNH Ribonuclease inhibitor
Thioreductase
TXN2 NM_012473
TXNDC11 NM_015914
TXNDC12 NM_015913
TXNDC15 NM_024715
TXNDC17 NM_032731
TXNDC9 NM_005783
TXNL1 NM_004786
TXNL4A NM_006701
TXNL4B NM_017853
TXNRD1 NM_003330
Structural
Cytoskeletal
ANXA6
ANXA7
ARPC1A Actin-related peptide
ARPC2
ARPC5L
CAPZA2
CAPZB
RHOA also implicated in regulation of cell cycle
RHOB
RHOT1 mitochondrial trafficking
RHOT2
TUBB Tubulin, beta polypeptide
WDR1 actin disassembly?
Organelle synthesis
A specialized form of cell signaling
BLOC1S1
BLOC1S2NM_173809
BLOC1S3NM_212550
BLOC1S4NM_018366
BLOC1S6NM_012388
AP1G1 NM_001128
AP1M1 NM_032493
AP2A1 NM_014203
AP2A2 NM_012305
AP2M1
AP2S1 NM_004069
AP3B1 NM_003664
AP3D1 NM_003938
AP3M1 NM_012095
AP3S1 NM_001284
AP3S2 NM_005829
AP4B1 NM_006594
AP5M1 NM_018229
ANXA6 Annexin 6
ANXA7 Annexin 7
AP1B1 Coated vesicles
CLTA Clathrin A (vesicles)
CLTB Clathrin B (vesicles)
CLTC
Mitochondrion
MTX2
Surface
AP2S1
CD81
GPAA1
LGALS9
MGAT2
MGAT4B
VAMP3
Cell adhesion
CTNNA1 NM_001903
CTNNB1
CTNNBIP1 NM_020248
CTNNBL1 NM_030877
CTNND1 NM_001085458 delta catenin
Channels and transporters
ABCB10 NM_012089
ABCB7 NM_004299
ABCD3 NM_002857
ABCE1 NM_002939
ABCF1 NM_001090
ABCF2 NM_005692
ABCF3 NM_018358
CALM1 Calmodulin grasps calcium ions
MFSD11 NM_024311 similar to MSFD10 aka TETRAN or tetracycline transporter-like protein
MFSD12 NM_174983
MFSD3 NM_138431
MFSD5 NM_032889
SLC15A4 NM_145648
SLC20A1 NM_005415
SLC25A11 mitochondrial oxoglutarate/malate carrier
SLC25A26 NM_173471
SLC25A28 NM_031212
SLC25A3 NM_002635
SLC25A32 NM_030780
SLC25A38 NM_017875
SLC25A39 NM_016016
SLC25A44 NM_014655
SLC25A46 NM_138773
SLC25A5 NM_001152
SLC27A4 NM_005094
SLC30A1 NM_021194
SLC30A5 NM_022902
SLC30A9 NM_006345
SLC35A2 NM_005660
SLC35A4 NM_080670
SLC35B1 NM_005827
SLC35B2 NM_178148
SLC35C2 NM_015945
SLC35E1 NM_024881
SLC35E3 NM_018656
SLC35F5 NM_025181
SLC38A2 NM_018976
SLC39A1 NM_014437
SLC39A3 NM_144564
SLC39A7 NM_006979
SLC41A3 NM_017836
SLC46A3 NM_181785
SLC48A1 NM_017842
Receptors
ACVR1 NM_001105 similar to ACVRL1 TGF Beta receptor family Rendu-Osler-Weber syndrome
ACVR1B NM_004302
CD23 FCER2 low affinity IgE receptor (lectin)
HLA/immunoglobulin/cell recognition
BAT1 aka DDX39B which is involved in RNA splicing
BSG Basigin Immunoglobulin Superfamily, extracellular metalloproteinase
MIF macrophage migration inhibitory factor
TAPBP
Kinases/signalling
ADRBK1 can downregulate response to epinephrine
AGPAT1 acyl 3 phosphoglycerol acyl transferase
ARF1
ARF3
ARF4
ARF5
ARL2 RAS Superfamily
CSF1 Colony stimulating factor not highly expressed constitutively at 5-12
CSK C-src tyrosine kinase
DCT dopachrome tautomerase
EFNA3
FKBP1A
GDI1 GDP Dissociation inhibitor (Rab family)
GNAS1 ubiquitously expressed, but differentially imprinted
GNAI2
HAX1 associated with tyrosine kinases
ILK Integrin linked kinase
MAPKAPK2
MAP2K2
MAP3K11
PITPNM Phosphatidylinositol transfer protein
RAC1 Ro GTPase involved with many signaling pathways
RAP1B GTPase involved with cell adhesion
RAGA Ras-related GTP Binding
STK19
STK24 Serine/Threonine Kinase
STK25
YWHAB Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide
YWHAH Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, h polypeptide
YWHAQ Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide
YWHAZ Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
Growth factors
AIF1
HDGF Hepatoma derived growth factor (translocates to nucleus)
HGS
LTBP4
VEGFB
ZFP36L1
Tissue necrosis factor
CD40 formerly TNFRSF5
Casein kinase
CSNK1E
CSNK2B
Miscellaneous
ALAS1 Aminolevulinic Acid Synthase type 1 (type 2 is erythroid and associated with porphyria)
ARHGEF2 Rho guanine nucleotide exchange factor
ARMET Mesencephalic astrocyte-derived neurotrophic factor
AES amino terminal enhancer of split
BECN1 involved in autophagy and partners with PI3K
BUD31 formerly Maternal G10 transcript
Creatine kinase CKB (ATP reservoir)
Cytidine deaminase questionable: not present in very high levels at all
CPNE1
ENSA (gene)
FTH1 Heavy chain of Ferritin
GDI2 rab/ras vesicular trafficking
GUK1 Guanylate kinase transfers phosphate from ATP to GMP
HPRT Hypoxanthine-guanine phosphoribosyltransferase
IFITM1 Induced by interferon, transmembrane protein
JTB (gene) Jumping translocation breakpoint
MMPL2
NME2 (formerly NM23B) Nucleoside diphosphate kinase
NONO
P4HB
PRDX1 peroxiredoxin (reduces peroxides)
PTMA Prothymosin
RPA2 Binds DNA during replication to keep it straightened out
SULT1A3 Sulfate conjugation (note: SULT1C is cited in earlier literature as being ubiquitous but this may be an example of different tags being used to refer to a common area of 2 closely related genes. If the tag is too short, then it may not be specific enough to truly specify one member of a gene family from another)
SYNGR2 Synaptogyrin (may participate in vesicle translocation)
Tetratricopeptide, TTC1 small glutamine rich tetratricopeptide
Open_reading_frame
C11Orf13
C14orf2
C21orf33
Sperm/Testis
Although this page is devoted to genes that should be ubiquitously expressed, this section is for genes whose current name reflects their relative upregulation in testes
SPAG7
SRM Spermidine synthase
TEGT Bax-1 inhibitor
DAZAP2 Deleted in azoospermia
MEA1 Male enhanced antigen
See also
Inducible gene
Genevestigator
Spatiotemporal gene expression
Essential proteins in protein complexes
Gene
Genome
Minimal genome
List of gene families
References
External links
Genes
Gene expression