Misplaced Pages

C22orf23
Identifiers
Aliases	C22orf23, EVG1, dJ1039K5.6, chromosome 22 open reading frame 23
External IDs	MGI: 1920774; HomoloGene: 13062; GeneCards: C22orf23; OMA:C22orf23 - orthologs
Gene location (Human) Chr. Chromosome 22 (human) Band 22q13.1 Start 37,943,050 bp End 37,953,669 bp
Gene location (Mouse) Chr. Chromosome 15 (mouse) Band 15 E1|15 37.7 cM Start 79,013,549 bp End 79,025,453 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in left testis sperm right testis testicle right uterine tube smooth muscle tissue muscle layer of sigmoid colon body of stomach C1 segment gonad Top expressed in seminiferous tubule olfactory epithelium spermatocyte spermatid neural layer of retina right kidney utricle proximal tubule ascending aorta Epithelium of choroid plexus More reference expression data BioGPS n/a
Gene ontology Molecular function protein binding molecular function Cellular component cellular component Biological process biological process Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 84645 27660 Ensembl ENSG00000128346 ENSMUSG00000033029 UniProt Q9BZE7 Q9D9S1 RefSeq (mRNA) NM_001207062 NM_032561 NM_138581 NM_001310576 NM_001310579 NM_001310581 RefSeq (protein) NP_001193991 NP_115950 NP_001297505 NP_001297508 NP_001297510 NP_613047 Location (UCSC) Chr 22: 37.94 – 37.95 Mb Chr 15: 79.01 – 79.03 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

C22orf23 (Chromosome 22 Open Reading Frame 23) is a protein which in humans is encoded by the C22orf23 gene. Its predicted secondary structure consists of alpha helices and disordered/coil regions. It is expressed in many tissues and highest in the testes and it is conserved across many orthologs.

Gene

Size and locus

C22orf23 is a gene found in homo sapiens. It is located on Chromosome 22 on the minus strand, map position 22q13.1. It spans 10,620 base pairs. Its mRNA transcript is 1988 base pars long and has 7 exons. Its predicted function is protein binding, and molecular function.

Common aliases

C22orf23's aliases are: UPF0193 Protein EVG1, DJ1039K5.6, EVG1 FLJ32787, and LOC84645.

Protein

Primary sequence

The protein encoded by the mRNA sequence is 217 amino acids in length and has a predicted molecular mass of 25 kDa. The predicted isoelectric point is 9.8. It is located in the nucleus.

Domains and motifs

It is predicted to be an intracellular protein and does not have any predicted transmembrane domains. Due to its location and lack of predicted transmembrane domains, the protein structure is likely a globular protein.

Post-Translational Modifications

C22orf23 has many predicted post-translational modifications such as: phosphorylation sites, cell attachment sequences, N-myristoylation sites, O-linked glycosylation sites, glycation sites, Ac-ASQK cleaved-acetylated sites, and Sumoylation sites. Many of the predicted phosphorylation sites were also predicted to be O-linked glycosylation sites thus the phosphorylation site could be blocked altering that domain's structure or function.

Secondary Structure

The predicted secondary structure consists of alpha helices and disordered/coil regions. The predicted secondary structure model has a 28% coverage of the amino acid sequence with a 42.9% confidence.

Homology

Paralogs

There are currently no known paralogs to C22orf23.

Orthologs

Orthologs can be found in most major groups of species ranging from most similar in primates to most distant in a member of phylum Chytridiomycota. This includes: mammals, reptiles, birds, amphibian, bony fish, cartilaginous fish, invertebrates, and fungi. Orthologs may have first appeared in plants or fungi however it is uncertain.

This table lists several orthologs for C22orf23 and includes their species name, common name, taxonomic order, accession number, sequence length, sequence similarity, and evolutionary date of divergence.

Expression

Promoter

The core promoter is GXP_7541220 (-), and its coordinates are 37953445-37954669 and it is 1225 base pairs long.

Tissue expression

Human expression

Protein expression is highest in the testes however it is also expressed at low levels in many other tissues such as: brain, kidney, stomach, skin, thyroid, urinary bladder, placenta, endometrium, esophagus, and appendix, bone marrow, adipose, lung, and ovary.

Ortholog expression

Expression in orthologs Rattus norvegicus, is expressed primarily in the testes with low levels of expression in the: kidneys, lungs, heart, and uterus. Mus musculus is expressed primarily in the adrenal and testes, and also notably expressed in the: bladder, abdomen, heart, lungs, ovaries, and mammary gland.

Interactions

Protein Interactions

There are several predicted protein interactions: Cyclin-D1-binding protein 1 which may regulate cell cycle progression, Vacuolar protein sorting-associated protein 28 homolog which is involved as a regulator of vesicular trafficking, UPF0739 protein C1orf74, and estrogen related receptor gamma. These interacting proteins were identified as either having direct interactions or physical associations. They were identified through a variety of detection methods including affinity chromatography, 2 hybrid prey pooling, and 2 hybrid array. It also has predicted protein interactions with SH3 domain containing 19, EvC ciliary complex subunit 1, RIMS binding protein 3B, RIMS binding protein 3C,TSSK6-activating co-chaperone protein, V-set and immunoglobulin domain containing 8, family with sequence similarity 124 member B, small nucleolar RNA host gene 28, and transmembrane protein 200B. Evidence suggesting a functional link for these interactions were supported through Co-mention on PubMed.

Clinical Significance

Disease Association

C22orf23 was identified as belonging to one of two groups of pooled serum samples in a study that analyzed the difference between serum glycoproteins of hepatocellular carcinoma and that of normal serum. Deletions of parts of C22orf23 (exons 3 and 4) and several other genes including SOX10 has been observed in patients with peripheral demyelinating neuropathy, central demyelinating leukodystrophy, Waardenburg Syndrome, and Hirschsprung disease and is therefore, suggested to be a potential factor involved in these ailments. C22orf23 was also mentioned in a study of mutation profiles from ER+ breast cancer samples taken from postmenopausal patience. There were mutations found that affected C22orf23 among many other genes. In a study of epigenetic alterations involved in coronary artery disease, C22orf23 was found to have altered epigenetic modifications which could be involved in novel genes in Coronary artery disease. In a study that attempts to predict imprinted genes that maybe linked to Human disorders, C22orf23 was identified as homologous of imprinted Gene candidates showing linkage to schizophrenia. In another study it was listed as being a potently regulated protein in uterine leiomyoma.

Mutations

There are a total of 3340 SNPs within the 5’ and 3’ UTR, introns, exons, as well as some genes near the 5’ and 3’ UTR. There is a total of 225 SNPs within the coding sequence. Some of the SNPs occur in conserved amino acids within the coding sequence and some reported have one or more types of validation. Some of the SNPs have high heterozygosity scores and thus have a presence in the population.

References

1. ^ GRCh38: Ensembl release 89: ENSG00000128346 – Ensembl, May 2017
2. ^ GRCm38: Ensembl release 89: ENSMUSG00000033029 – Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. ^ "C22orf23 Gene(Protein Coding)". GeneCards Human Gene Database. 2019-05-05.
6. ^ "Chromosome 22 open reading frame 23 (C22orf23)". www.ncbi.nlm.nih.gov. Retrieved 2019-05-02.
7. "Homo sapiens chromosome 22 open reading frame 23 (C22orf23), transcript variant 1, mRNA". Retrieved 2019-05-01.
8. ^ "C22orf23 Gene". Gene Cards Human Gene Database. Archived from the original on 2011-11-28. Retrieved 2019-05-01.
9. "WikiGenes - Collaborative Publishing". WikiGenes - Collaborative Publishing. Archived from the original on 2018-09-13. Retrieved 2019-05-04.
10. ^ "Cell atlas - C22orf23 - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2019-05-04.
11. "ExPASy - Compute pI/Mw tool". web.expasy.org. Retrieved 2019-05-04.
12. "TMpred - Prediction of Transmembrane Regions and Orientation". ExPASy Bioinformatics Resource Portal. 2019-05-05. Archived from the original on 2019-03-05. Retrieved 2019-05-06.
13. "SAPS - Statistical Analysis of Protein Sequences". EMBL-EBI -SAPS. 2019-05-05.
14. ^ "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-05-04.
15. "NetPhos 3.1 Server". DTU Bioinformatics Department of Bio and Health Informatics. 2019-05-05.
16. "Motif Scan". Myhits. 2019-05-05.
17. "NetOGlyc 4.0 Server". DTU Bioinformatics Department of Bio and Health Informatics. 2019-05-05.
18. "NetGlycate 1.0 Server". DTU Bioinformatics Department of Bio and Health Informatics. 2019-05-05.
19. "GPS SUMO - prediction of SUMOylation & SUMO- binding Motifs". GPS. 2019-05-05. Archived from the original on 2013-05-10. Retrieved 2019-05-06.
20. "SUMOplot™ Analysis Program". ABGENT Wuxi App Tec Company. 2019-05-05. Archived from the original on 2005-01-03.
21. "CFSSP - Chou & Fasman secondary structure prediction server". 2019-05-04.
22. "A Protein Secondary Structure Prediction Server". Jpred 4 incorporating Jnet. 2019-05-04.
23. "SOPMA SECONDARY STRUCTURE PREDICTION METHOD". PRAB- Gerland Rhone-Alpes Bioinformatics Pole Gerland Site - Institute of biology and protein chemistry. 2019-05-04.
24. "GOR IV SECONDARY STRUCTURE PREDICTION METHOD". PRAB- Gerland Rhone-Alpes Bioinformatics Pole Gerland Site - Institute of biology and protein chemistry. 2019-05-04.
25. "BLAT Search Genome". University of California Santa Cruz Genome Institute - UCSC Genome Browser-Blat. 2019-05-05.
26. ^ "Standard Protein BLAST". NCBI - Protein BLAST. 2019-05-05.
27. "HomoloGene". NCBI - HomoloGene. 2019-05-05.
28. "TimeTree of Life". Timetree The Timescale of Life. 2019-05-05.
29. Russ C, Lang BF, Chen Z, Gujja S, Shea T, Zeng Q, Young S, Cuomo CA, Nusbaum C (August 2016). "Genome Sequence of Spizellomyces punctatus". Genome Announcements. 4 (4): e00849-16. doi:10.1128/genomeA.00849-16. PMC 4991717. PMID 27540072.
30. "Genomatix". Genomatix Software Suite v3.10. 2019-05-05.
31. "EST Profile - Hs.517612 - C22orf23". NCBI - Unigene. 2019-05-05.
32. "C22orf23 chromosome 22 open reading frame 23 [ Homo sapiens (human) ]". NCBI - Gene. 2019-05-05.
33. "C22orf23". The Human Protein Atlas. 2019-05-05.
34. "RGD1359634 similar to RIKEN cDNA 1700088E04 [ Rattus norvegicus (Norway rat) ]". NCBI - Gene. 2019-05-05.
35. "1700088E04Rik RIKEN cDNA 1700088E04 gene [ Mus musculus (house mouse) ]". NCBI - Gene. 2019-05-05.
36. ^ "NCBI". National Center for Biotechnology Information - NCBI. 2019-05-05.
37. "PSICQUIC View". EMBL-EBI. 2019-05-05.
38. "Mentha". Mentha The interactome browser. 2019-05-05.
39. "String". STRING Database. 2019-05-05.
40. Gao HJ, Chen YJ, Zuo D, Xiao MM, Li Y, Guo H, Zhang N, Chen RB (September 2015). "Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum". Cancer Biology & Medicine. 12 (3): 246–54. doi:10.7497/j.issn.2095-3941.2015.0010. PMC 4607824. PMID 26487969.
41. Wenzhi H, Ruijin W, Jieliang L, Xiaoyan M, Haibo L, Xiaoman W, Jiajia X, Shaoying L, Shuanglin L, Qing L (October 2015). "Heterozygous deletion at the SOX10 gene locus in two patients from a Chinese family with Waardenburg syndrome type II". International Journal of Pediatric Otorhinolaryngology. 79 (10): 1718–21. doi:10.1016/j.ijporl.2015.07.034. PMID 26296878.
42. Bondurand N, Dastot-Le Moal F, Stanchina L, Collot N, Baral V, Marlin S, Attie-Bitach T, Giurgea I, Skopinski L, Reardon W, Toutain A, Sarda P, Echaieb A, Lackmy-Port-Lis M, Touraine R, Amiel J, Goossens M, Pingault V (December 2007). "Deletions at the SOX10 gene locus cause Waardenburg syndrome types 2 and 4". American Journal of Human Genetics. 81 (6): 1169–85. doi:10.1086/522090. PMC 2276340. PMID 17999358.
43. Pascal, Gellert (December 2014). "Abstract S1-04: Exome sequencing of post-menopausal ER+ breast cancer (BC) treated pre-surgically with aromatase inhibitors (AIs) in the POETIC trial (CRUK/07/015". Cancer Research. 75 (9 Supplement): S1-04. doi:10.1158/1538-7445.SABCS14-S1-04.
44. Sharma P, Garg G, Kumar A, Mohammad F, Kumar SR, Tanwar VS, Sati S, Sharma A, Karthikeyan G, Brahmachari V, Sengupta S (May 2014). "Genome wide DNA methylation profiling for epigenetic alteration in coronary artery disease patients". Gene. 541 (1): 31–40. doi:10.1016/j.gene.2014.02.034. PMID 24582973.
45. Luedi PP, Hartemink AJ, Jirtle RL (June 2005). "Genome-wide prediction of imprinted murine genes". Genome Research. 15 (6): 875–84. doi:10.1101/gr.3303505. PMC 1142478. PMID 15930497.
46. Ahn WS, Kim KW, Bae SM, Yoon JH, Lee JM, Namkoong SE, Kim JH, Kim CK, Lee YJ, Kim YW (December 2003). "Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis". International Journal of Experimental Pathology. 84 (6): 267–79. doi:10.1111/j.0959-9673.2003.00362.x. PMC 2517572. PMID 14748746.
47. "dbSNP Short Genetic Variations". NCBI. 2019-05-05.

• Genes on human chromosome 22
• Proteins