Persius/hicric huggingface dataset:
C9orf25
Chromosome 9 open reading frame 25 (C9orf25) is a domain that encodes the FAM219A gene. The terms FAM219A and C9orf25 are aliases and can be used interchangeably. The function of this gene is not yet completely understood.

# Gene

## Location
In humans, C9orf25 is located at the 9p13.3 position on chromosome 9. The gene is encoded on the sense strand (-) spanning the chromosomal locus from base pair 34,502,909 to 34,398,027. The span of the gene is 104,882 base pairs

## Transcript variants
In humans there are 8 main transcript variants of the FAM219A gene. All of these transcripts have varying lengths and splice sites with transcript variant 1 being the longest and most abundant. Only four of these transcripts encode for a protein product.

# Homology

## Orthologs
The C9orf25 gene has orthologs in a wide variety of Eukaryotic organisms, including invertebrates. This gene has not been found in plants, fungi or protists. C9orf25 is a slowly evolving gene. It is also highly conserved through out all of its known orthologs.

## Paralogs
C9orf25 has a paralog FAM219B which is located on the long arm of chromosome 9 and is 198 amino acids long. The C9orf25 and FAM219B genes duplicated and diverged between 684 and 797 million years ago.

# Protein

## General properties
The C9orf25 protein is composed of 185 amino acids. It has a molecular weight of 20.4 kilodaltons and an isoelectric point of 4.47. It is a member of the FAM219 super family. The entire protein is still considered to be a domain of unknown function.

## Protein localization
C9orf25 has no signal sequence and remains in the cytosol.

## Conserved motifs and post-translational modifications
The following are experimental post-transitional modifications for the C9orf25 protein:
- 6 predicted Serine phosphorylation sites
- 1 predicted Tyrosine phosphorylation site
- 1 predicted prenylation site

## Secondary structure
The secondary structure of the gene is predicted to have two stretches of alpha helices and one beta strand. The majority of the secondary structure of gene is random coils.

## Expression
The C9orf25 gene has medium to high expression in most tissues of the body. The gene has particularly high expression in the nervous, digestive and male reproductive systems.

## Interacting proteins
The C9orf25 gene has many different interactions with a variety of other proteins that have an assortment of functions. The main ones that are listed on at least two reviewed sources are shown below.

# Clinical significance
The C9orf25 protein is associated with several disease causing proteins, however does not seem to be responsible for disease on its own.  The gene seems to have higher expression in metastatic cells.
C9orf64
C9orf64 (Chromosome 9 open reading frame 64) is a gene located on chromosome 9, that in humans encodes the protein queuosine salvage protein. The function and biological process of the queuosine salvage protein is not well understood by the scientific community, but some evidence from orthologs indicates it may be involved in tRNA processing. The most common mRNA contains 4 coding exons, and it has 2 additional alternatively spliced exons. C9orf64 has been found in 5 different splice variants.
Expression of this gene is highest in the duodenum and small intestine, and it is also expressed in 24 other tissues. 
22 variants have been annotated in the NIH Database, ClinVar, linked to disease conditions such as seizures, developmental delay, and muscular hypotonia.

# Protein
Queuosine salvage protein is 341 amino acids long with a molecular weight of 39,029 Daltons and an isoelectric point of 5.61. It is a member of the DUF2419 superfamily. The DUF position on the human protein is from amino acid 53 to 341.
Bioinformatic tools at ExPASy predicted a second peroxisomal targeting signal.

# Gene locus
C9orf64 is located on chromosome 9q21.32. The genes closest to C9orf64 on the long arm of chromosome 9 include GKAP1, KIF27, HNRNPK, RMI1, and a MicroRNA  MIR7-1.

# Homology
C9orf64 is only found in eukaryotes. Orthologs have been found from primates to fungi and plants.
CA-19-9

# Overview
CA-19-9 is a tumor marker.

# Interpretation
CA 19-9 is elevated in most patients with advanced pancreatic cancer, but it may also be elevated in other cancers, conditions, and diseases such as colorectal cancer, lung cancer, gallbladder cancer, gallstones, pancreatitis, cystic fibrosis, and liver disease.
Other causes of bile duct obstruction may also cause very high CA 19-9 levels, which fall when the blockage is cleared.
If the bile ducts are blocked, wait a week or two after the blockage is removed or treated to check CA 19-9 levels.

# Differential Diagnosis
In alphabetical order.  

## Increased level of CA-19-9

### Malignant Diseases
- Biliary tract carcinoma
- Breast Cancer
- Bronchial carcinoma
- Colorectal Cancer
- Gastric carcinoma
- Liver carcinoma
- Ovarian Cancer
- Pancreatic Cancer
- Uterine Cancer

### Non-Malignant Diseases
- Cholecystitis
- Choledocholithiasis
- Cirrhosis
- Pancreatitis
- Pleural Effusions

# Related chapters
- CA 19-9
CACNA1G
Calcium channel, voltage-dependent, T type, alpha 1G subunit, also known as CACNA1G or Cav3.1 is a protein which in humans is encoded by the CACNA1G gene.

# Function
Voltage-dependent calcium channels can be distinguished based on their voltage-dependence, deactivation, and single-channel conductance. Low-voltage-activated calcium channels are referred to as 'T' type because their currents are both transient, owing to fast inactivation, and tiny, owing to small conductance. T-type channels are thought to be involved in pacemaker activity, low-threshold calcium spikes, neuronal oscillations and resonance, and rebound burst firing.

# Interactive pathway map
Click on genes, proteins and metabolites below to link to respective Wikipedia articles. 
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CACNA1H
Calcium channel, voltage-dependent, T type, alpha 1H subunit, also known as CACNA1H, is a protein which in humans is encoded by the CACNA1H gene.

# Function
This gene encodes Cav3.2, a T-type member of the 1 subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of 1, 2, , and  subunits in a 1:1:1:1 ratio. The 1 subunit has 24 transmembrane segments and forms the pore through which ions pass into the cell. There are multiple isoforms of each of the proteins in the complex, either encoded by different genes or the result of alternative splicing of transcripts. Alternate transcriptional splice variants, encoding different isoforms, have been characterized for the gene described here.

# Clinical significance
Studies suggest certain mutations in this gene lead to childhood absence epilepsy (CAE). Variants of Cav3.2 with increased channel activity contribute to susceptibility to idiopathic generalized epilepsy (IGE), but are not sufficient to induce epilepsy on their own.  The SFARIgene database lists CACNA1H with an autism score of 2.1, indicating a candidate causal relationship with autism.
CAPRIN2
caprin family member 2, also known as CAPRIN2, is a human gene.
The protein encoded by this gene may be involved in the transitioning of erythroblasts from a highly proliferative state to a terminal phase of differentiation. High level expression of the encoded protein can lead to apoptosis. Several transcript variants encoding different isoforms have been found for this gene.

# Model organisms
Model organisms have been used in the study of CAPRIN2 function. A conditional knockout mouse line, called Caprin2tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty two tests were carried out on mutant mice, however no significant abnormalities were observed.
CCDC137
Coiled-coil domain containing 137 is a protein that in humans is encoded by the CCDC137 gene.

# Model organisms
Model organisms have been used in the study of CCDC137 function. A conditional knockout mouse line, called Ccdc137tm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty five tests were carried out on mutant mice and two significant abnormalities were observed. No homozygous mutant embryos were recorded during gestation and, in a separate study, no homozygous animals were observed at weaning. The remaining tests were carried out on adult heterozygous mutant animals, but no further abnormalities were seen.
CCDC176
Basal body-orientation factor 1 (BBOF1) is a protein that in humans is encoded by the gene CCDC176, which is located on the plus strand of chromosome 14 at 14q24.3. CCDC176 is neighbored by ALDH6A1 and ENTPD5 at the same locus. 
The mRNA is 3123 base pairs long and has 12 exons, the protein is 529 amino acids long and has a molecular weight of 61987 Da and a predicted isoelectric point of 9.07 in humans.

# Homology and evolution
CCDC176 has no known paralogs and is orthologous in primates, mammals, birds, reptiles, amphibians, fish, all the way back to invertebrates, a fungi parasite and a proteobacteria. The domain found to be homologous is the DUF4515, a domain of unknown function.

# Protein function and characteristics
This basal body protein has been shown in multiciliated cells to align and maintain cilia orientation in response to flow. This protein may also act by mediating a maturation step that stabilizes and aligns cilia orientation.
No other genes or proteins have been found that encode basal body orientation factors. A similar set of genes, tubulin tyrosine ligase-like genes 3 and 6, has been found in zebrafish that maintain cilia structure and motility. These genes belong to the TTL (tubulin tyrosine ligase) family.
BBOF1 has two coiled coil domains, one that is 117 amino acids in length at the position 85-201 and the second is 91 amino acids in length at the position 271-361. There is also a region of interest located at the position 77-270 and is named DUF4515, a domain of unknown function belonging to the family of pfam14988.
There are three predicted protein-protein interactions concerning CCDC176. The most prevalent and most likely interaction is with LIG4, a human gene that encodes the protein DNA Ligase IV. Two experiments in a publication of 1030 unique reactions support the LIG4-CCDC176 interaction. The second and third predicted interactions are NRF1 and HYLS1.
The predicted secondary structure of BBOF1 in humans is as follows:  87.1% alpha helix, 63.9% beta sheet, and 15.7% beta turn.

# Expression, research, and clinical significance
CCDC176 has known expression in the human testis, cerebellum, and lung tissues.
There are six articles of research related to the gene CCDC176, with four out of six being large-scale sequencing, one article not naming the gene or protein, and one article with only the abstract available. This last article, Global, in vivo, and site-specific phosphorylation dynamics in signaling networks, is the only article that directly mentions the protein of interest and it does so only once. This study detected 6,600 phosphorylation sites on 2,244 proteins.
Expression data from different health states in humans predicts high expression of CCDC176 in glioma. 
The interaction data concerning CCDC176 and LIG4 came from a publication studying protein-protein interaction involved with the DNA damage response network in association with cancer
CCDC186
CCDC186 is a protein that in humans is encoded by the CCDC186 gene  The CCDC186 gene is also known as the CTCL-tumor associated antigen with accession number NM_018017.

# Gene

## Location
CCDC186 has the chromosome location of 10q25.3 and is 53,750 bases in size oriented on the minus strand. PSORTII Protein k-NN Prediction indicated that C10orf118 is 65.2% of the time nuclear, 17.4% cytosolic, 8.7% mitochondrial, 4.3% vesicles of secretory system, and 4.3% endoplasmic reticulum.

## Expression
Analysis of gene expression in humans and other species indicates C10orf118 is ubiquitously expressed in all tissue types at varying developmental stages. An EST profile from NCBI displayed the greatest expression in bone marrow, kidneys, and the prostate cell lines. Breakdown by health state indicates high expression of C10orf118 in bladder carcinoma and prostate cancer.

# Protein

## General Properties
The protein of CCDC186 (NP_060487) is 898 amino acids in length. The predicted molecular weight is 103.7kdal and the isoelectric point is predicted to be 5.92.

## Composition
A serine rich region is observed in amino acids 710-747. A compositional analysis revealed that C10orf118 is Proline (1.1%) poor and Glutamic acid (14.1%) and Lysine (12.0%) rich.

## Interactions
CCDC186 protein was found to interact with proteins PLEKAH5, Ezra, GAMMAHV.ORF23, and SMAD3.

## Homology
Orthologous sequences of CCDC186 were not found to be in bacteria, archea, protist, or plants. CCDC186 has no human paralogs. The date of divergence for the orthologous sequences highly correlates with the sequences similarity in that the percent identity decreases as you go back in time. Closely related orthologs include mammals and birds and moderately related orthologs include other vertebrates such as fish, reptiles, and amphibians. Distantly related orthologous sequences are primarily observed in invertebrates.

## Motifs

## Post Translational Modification
CCDC186 is predicted to undergo multiple posttranslational modifications including predicted O-beta-GlcNAc attachment, phosphorylation, a nuclear export signal, glycation of lysines, GlcNAc O-glycosylation, N-glycosylation, and NetCorona sites.

## Clinical significance
Prior research indicates that the open reading frame of C10orf118 is linked to cutaneous T-cell lymphoma by a tumor antigen L14-2. The protein CCDC186 is also found at higher than normal levels in the breast cancer cell line BC 8701.
CCDC90B
Coiled coil domain containing 90B, also known as CCDC90B, is a protein encoded by the CCDC90B gene.

# Gene
CCDC90B is located on chromosome 11 in humans. It is neighbored by:
- PCF11, a mammalian pre-mRNA cleavage complex 2 protein
- ANKRD42, ankyrin repeat protein involved with calcium ion bonding
- BC070093
- DLG2, a member of the membrane-associated guanylate kinase (MAGUK) family

# Protein

## Structure
This protein is characterized by the presence of a domain of unknown function, DUF1640. This domain is a characteristic of the entire protein with the exception of the first twenty-three amino acid residues - MNSRQAWRLFLSQGRGDRWVSRP - which are a mitochondrial targeting site and cleaved.
The protein has seven predicted alpha helices, a characteristic of coiled-coil proteins.

## Predicted Properties
Molecular Weight: 26.72 kDa
Isoelectric point: 7.5
Transmembrane Helices: None
Post-translation modifications:

## Cellular Location
CCDC90B is presumably a mitochondrial protein. It is predicted to contain at least three specific phosphorylation sites: Protein Kinase C Phosphorylation sites, Casein Kinase II Phosphorylation sites, and cAMP/cGMP Dependant Phosphorylation sites.
CCNDBP1
Cyclin-D1-binding protein 1 is a protein that in humans is encoded by the CCNDBP1 gene.
This gene was identified by the interaction of its gene product with Grap2, a leukocyte-specific adaptor protein important for immune cell signaling. The protein encoded by this gene was shown to interact with cyclin D. Transfection of this gene in cells was reported to reduce the phosphorylation of Rb gene product by cyclin D-dependent protein kinase, and inhibit E2F1-mediated transcription activity. This protein was also found to interact with helix-loop-helix protein E12 and is thought to be a negative regulator of liver-specific gene expression. Two alternatively spliced variants, which encode distinct isoforms, have been reported.

# Interactions
CCNDBP1 has been shown to interact with GRAP2 and Cyclin D1.
CD200R1
Cell surface transmembrane glycoprotein CD200 receptor 1 is a protein that in humans is encoded by the CD200R1 gene. CD200R1 is expressed on the surface of myeloid cells  and CD4+ T cells. It interacts with CD200 transmembrane glycoprotein that can be expressed on variety of cells including neurons, epithelial cells, endothelial cells, fibroblasts, and lymphoid cells.
CD200R1 activation regulates the expression of pro-inflammatory molecules such as tumor necrosis factor (TNF-alpha), interferons, and inducible nitric oxide synthase (iNOS).

# Function
This gene encodes a receptor for the OX-2 membrane glycoprotein. Both the receptor and substrate are cell surface glycoproteins containing two immunoglobulin-like domains. This receptor is restricted to the surfaces of myeloid lineage cells and the receptor-substrate interaction may function as a myeloid downregulatory signal. Mouse studies of a related gene suggest that this interaction may control myeloid function in a tissue-specific manner. Alternative splicing of this gene results in multiple transcript variants.
CDK2AP1
Cyclin-dependent kinase 2-associated protein 1 is an enzyme that in humans is encoded by the CDK2AP1 gene.

# Function
The protein encoded by this gene is a specific CDK2-associated protein, which is thought to negatively regulate CDK2 activity by sequestering monomeric CDK2, and targeting CDK2 for proteolysis. This protein was found to also interact with DNA polymerase alpha/primase and mediate the phosphorylation of the large p180 subunit, which suggested the regulatory role in DNA replication during S phase of the cell cycle. A similar gene in hamster was isolated from, and functions as a growth suppressor of normal keratinocytes.

# Interactions
CDK2AP1 has been shown to interact with Cyclin-dependent kinase 2.
It interacts with unnamed protein product (BC006130) which may mediate inhibitory effect of CDK2AP1 on cell proliferation.
CEACAM1
Carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) (CEACAM1) also known as CD66a (Cluster of Differentiation 66a), is a human glycoprotein, and a member of the carcinoembryonic antigen (CEA) gene family.

# Function
This gene encodes a member of the carcinoembryonic antigen (CEA) gene family, which belongs to the immunoglobulin superfamily. Two subgroups of the CEA family, the CEA cell adhesion molecules and the pregnancy-specific glycoproteins, are located within a 1.2 Mb cluster on the long arm of chromosome 19. Eleven pseudogenes of the CEA cell adhesion molecule subgroup are also found in the cluster. The encoded protein was originally described in bile ducts of liver as biliary glycoprotein. Subsequently, it was found to be a cellcell adhesion molecule detected on leukocytes, epithelia, and endothelia. The encoded protein mediates cell adhesion via homophilic as well as heterophilic binding to other proteins of the subgroup. Multiple cellular activities have been attributed to the encoded protein, including roles in the differentiation and arrangement of tissue three-dimensional structure, angiogenesis, apoptosis, tumor suppression, metastasis, and the modulation of innate and adaptive immune responses. Multiple transcript variants encoding different isoforms have been reported, but the full-length nature of only two has been determined.
In melanocytic cells CEACAM1 gene expression may be regulated by MITF.

# Interactions
CEACAM1 has been shown to interact with PTPN11 and Annexin A2.
CEACAM3
Carcinoembryonic antigen-related cell adhesion molecule 3 (CEACAM3) also known as CD66d (Cluster of Differentiation 66d), is a member of the carcinoembryonic antigen (CEA) gene family..
This gene encodes a member of the family of carcinoembryonic antigen-related cell adhesion molecules (CEACAMs), which are used by several bacterial pathogens to bind and invade host cells. The encoded transmembrane protein directs phagocytosis of several bacterial species that is dependent on the small GTPase Rac. It is thought to serve an important role in controlling human-specific pathogens by the innate immune system. Alternatively spliced transcript variants have been described, but their biological validity has not been determined.

# Use
CEACAM3 is expressed exclusively on granulocytes and used as granulocyte marker.
CFAP157
Cilia and flagella associated protein 157 (CFAP157) also known as chromosome 9 open reading frame 117 (c9orf117) is a protein that in humans is encoded by the CFAP157 gene.
CFAP157 gene is "specifically required during spermatogenesis for flagellum morphogenesis and sperm motility and may be required to suppress the formation of supernumerary axonemes and ensure a correct ultrastructure," according to UniProt.

# Gene

## Location
CFAP157 is located on chromosome 9, 9q34.11 in human from base pair 127,706,989 to base pair 127,716,002.

## Features
The size of the gene is 9,013 bases, and the orientation is plus strand. The gene holds 9 exons.

# mRNA
The most common variant of mRNAs of CFAP157 contains 1,722 base pairs.

## Expression
CFAP157 is expressed in many human body tissues such as cervix, lung, testis, and uterus. People who have uterine tumor are likely to have an expression in CFAP157. This gene is expressed in both adults and fetuses.

# Protein
There are 520 amino acids in CFAP157 in human. The protein is glutamine extremely rich, and glycine poor. The protein is quite neutral with the isoelectric point at pH 7.4. The average mass of the protein is estimated to be 60,531.748 Da, and the absorption coefficient is estimated to be 25,440 M1 cm1.
CFAP157 is primarily composed of -helices, and there is no transmembrane helix. The protein structure making program called Phyre is used to create the predicted structure of CFAP157.

# Homology
There is no known paralog for CFAP157 in human. CFAP157 has numerous orthologs. The following table contains some of orthologs including human, common chimpanzee, rhesus macaque, cattle, dog, mouse, rat, tropical clawed frog, and zebra fish.

# Interacting Proteins
P14335 (Kunjin virus strain MRM61C) is the virus that interacts with CFAP157 via two-hybrid screening. Kunjin virus is not as severe as other viruses, but this is a noticeable discovery because it is possible to exploit the interaction to develop new types of medicine. Researchers at the University of Queensland discovered a new medical use for the Kunjin virus in 2005, and the possible treatments include HIV/cancer vaccines.