C13orf38

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Predicted tertiary structure of protein C13orf38 Predicted Structure.png
Predicted tertiary structure of protein C13orf38

C13orf38 is a protein found in the thirteenth chromosome with an open reading frame number 38. It is 139 amino acids long. The protein goes by a number of aliases CCDC169-SOHLH2 and CCDC169. The protein is found to be over expressed in the testis of humans. [1] It is not known what the exact function of the protein is at this current time. The human CCDC169 gene contains 753 nucleotides. C13orf contains a domain of unknown function DUF4600. which is conserved in between nucleotide interval 1-79. The protein contains 139 amino acids.

Contents

Aliases

Known aliases are CCDC169 and CCDC169-SOHLH2. SOHLH refers to the suspected role in oogenesis and spermatogenesis. CCDC refers to the structure of the domain the protein, which is a coil-coil domain containing protein. Isoforms: C13orf38 has seven isoforms, a through e. The most common isoform is isoform b. CCDC169 isoform b gene codes for the C13orf38 protein. [2] Isoform b is the most common isoform.

Protein regulation

There is evidence that the protein is retained in the nucleus. There are several leucine-rich nuclear export signals in the amino acid sequence of the protein. [3] Making it likely to be retained in the nucleus after transcription.

Gene expression

Tissue expression

C13orf38 is over expressed in the testis of humans. It has very weak expression data in the bone marrow, brain, and vascular tissues. It is expressed in several types of tumors – brain, lung, and germ cell tumors. It can also be expressed in leukemia cells.

Antibodies

There are antibodies available that are polyclonal. [4] The antibodies come from a rabbit host sold by Bioss antibodies. The molecular weight is 25kDa. [5]

Homologs and paralogs

Homologs were found mostly in primates. The homolog with the furthest divergence would be the Hood coral, which predates humans by 686 million years.

There are two low identity paralogs and two hypothetical protein paralogs found through the sequencing of the human genome.

Genetic divergence

Diverges 432 million years ago from Zebra fish. [6] The most divergent species would be the Hood coral, Stylophora pistillata, at 686 million years ago.

Interacting proteins

Protein [7] annotationscore
AGPAT11-acyl-sn-glycerol-3-phosphate acyltransferase alpha; Converts lysophosphatidic acid (LPA) into phosphatidic acid by incorporating an acyl moiety at the sn-2 position of the glycerol backbone; 1-acylglycerol-3-phosphate O-acyltransferases0.471
BAIAP3BAI1 associated protein 3; C2 domain containing0.708
CLMPCXADR-like membrane protein; May be involved in the cell-cell adhesion. May play a role in adipocyte differentiation and development of obesity. Is required for normal small intestine development; I-set domain containing0.526
GABRQGamma-aminobutyric acid receptor subunit theta; GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel; Gamma-aminobutyric acid type A receptor subunits0.695
KCNK12Potassium channel subfamily K member 12; Probable potassium channel subunit. No channel activity observed in heterologous systems. May need to associate with another protein to form a functional channel (By similarity); Potassium two pore domain channel subfamily K0.677
NEMFNuclear export mediator factor NEMF; Component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation. NEMF is responsible for selective recognition of stalled 60S subunits by recognizing an exposed, nascent chain-conjugated tRNA moiety. NEMF is important for the stable association of LTN1 to the complex. May indirectly play a role in nuclear export0.572
TRIM68E3 ubiquitin-protein ligase TRIM68; Functions as a ubiquitin E3 ligase. Acts as a coactivator of androgen receptor (AR) depending on its ubiquitin ligase activity; Ring finger proteins0.559
VAV3Guanine nucleotide exchange factor VAV3; Exchange factor for GTP-binding proteins RhoA, RhoG and, to a lesser extent, Rac1. Binds physically to the nucleotide-free states of those GTPases. Plays an important role in angiogenesis. Its recruitment by phosphorylated EPHA2 is critical for EFNA1- induced RAC1 GTPase activation and vascular endothelial cell migration and assembly (By similarity). May be important for integrin-mediated signaling, at least in some cell types. In osteoclasts, along with SYK tyrosine kinase, required for signaling through integrin alpha-v/beta-1 (ITAGV-ITGB1), a [...]0.522
WBSCR17Polypeptide N-acetylgalactosaminyltransferase 17; May catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor0.685
ZNF562Zinc finger protein 562; May be involved in transcriptional regulation; Zinc fingers C2H2-type0.658

Experimental data

Cdcc169 has been used in a variety of tissue expression experiments. One study was done on a variety of tissues in order to show that gene expression in the mid-range of tissue expression can give a strong clue to the function of a gene. The study covered and analyzed set of 62,839 probe sets in 12 representative normal human tissues. [8] 0 represents housekeeping genes and 1 is for tissue specific genes. CCDC 169 was found not to have housekeeping gene type expression. It was tissue specific and appeared in the prostate.

A systematic survey of gene expression in 115 human tissue samples representing 35 different tissue types. The study used cDNA micro-arrays representing approximately 26,000 different human genes. [9] The study included Ccdc169, which showed a strong positive expression in the testes. This study goal was to find a baseline which could be used to help identify diseased tissue and look at genes with tissue specific expression and how those can be used as markers for detecting diseased and injured tissue in organs. Could be used in anticancer therapy.

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References

  1. ↑ Fagerberg, Linn; Hallström, Björn M.; Oksvold, Per; Kampf, Caroline; Djureinovic, Dijana; Odeberg, Jacob; Habuka, Masato; Tahmasebpoor, Simin; Danielsson, Angelika (2014). "Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics". Molecular & Cellular Proteomics. 13 (2): 397–406. doi: 10.1074/mcp.M113.035600 . ISSN   1535-9476. PMC   3916642 . PMID   24309898.
  2. ↑ "CCDC169 coiled-coil domain containing 169 [Homo sapiens (human)] – Gene – NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-05-15.
  3. ↑ la Cour, Tanja; Kiemer, Lars; Mølgaard, Anne; Gupta, Ramneek; Skriver, Karen; Brunak, Søren (2004). "Analysis and prediction of leucine-rich nuclear export signals". Protein Engineering, Design and Selection. 17 (6): 527–536. doi: 10.1093/protein/gzh062 . ISSN   1741-0134. PMID   15314210.
  4. ↑ "CCDC 169". www.genecards.org. Retrieved 2019-05-15.
  5. ↑ "C13orf38 Antibody bs-9613R from Bioss Inc. | Biocompare.com". www.biocompare.com. Retrieved 2019-05-15.
  6. ↑ dos Reis, Mario; Thawornwattana, Yuttapong; Angelis, Konstantinos; Telford, Maximilian J.; Donoghue, Philip C.J.; Yang, Ziheng (2015). "Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales". Current Biology. 25 (22): 2939–2950. Bibcode:2015CBio...25.2939D. doi:10.1016/j.cub.2015.09.066. PMC   4651906 . PMID   26603774.
  7. ↑ "Figure 5: Protein-protein interaction network based on STRING analysis". doi: 10.7717/peerj.6321/fig-5 .{{cite journal}}: Cite journal requires |journal= (help)
  8. ↑ Yanai, I.; Benjamin, H.; Shmoish, M.; Chalifa-Caspi, V.; Shklar, M.; Ophir, R.; Bar-Even, A.; Horn-Saban, S.; Safran, M. (2005-03-01). "Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification". Bioinformatics. 21 (5): 650–659. doi: 10.1093/bioinformatics/bti042 . ISSN   1367-4803. PMID   15388519.
  9. ↑ Shyamsundar, Radha; Kim, Young H; Higgins, John P; Montgomery, Kelli; Jorden, Michelle; Sethuraman, Anand; van de Rijn, Matt; Botstein, David; Brown, Patrick O (2005). "A DNA microarray survey of gene expression in normal human tissues". Genome Biology. 6 (9): 404. doi: 10.1186/gb-2005-6-9-404 . ISSN   1465-6906. PMC   1242207 . PMID   15774023.
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