Biology:C16orf78

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Short description: Protein-coding gene in the species Homo sapiens

Uncharacterized protein C16orf78(NP_653203.1) is a protein that in humans is encoded by the chromosome 16 open reading frame 78 gene.[1]

Gene

The C16orf78 gene(123970) is located at 16q12.1 on the plus strand, spanning 25,609 bp from 49,407,734 to 49,433,342.[2]

mRNA

There is one mRNA transcript (NM_144602.3) and no other known splice isoforms. There are 5 exons, totaling a length of 1068 base pairs.[2]

Protein

Sequence

C16orf78 is 265 amino acids long with a predicted molecular weight of 30.8 kDal and pI of 9.8.[3] It is rich in both methionine and lysine, composed of 6.4% methionine and 13.6% lysine.[4] This methionine richness has been hypothesized to serve as a mitochondrial antioxidant.[5]

Post-Transnational Modifications

There are four verified ubiquitination sites and three verified phosphorylation sites.[6][7]

Diagram of C16orf78 protein with ubiquitination sites marked in red and phosphorylation sites marked in gray.[8]

Structure

Predictions of C16orf78's secondary structure consist primarily of alpha helices and coiled coils.[9][10][11] Phyre2 also predicted C16orf78 is primarily helical, but 253 of 265 amino acids were modeled ab initio so the confidence of the model is low.[12]

Phyre2 generated model of C16orf78 rendered in Chimera.

Subcellular Localization

C16orf78 is predicted to be localized to the cell nucleus.[13] There is also a predicted bipartite nuclear localization signal.[14]

Expression

C16orf78 has restricted expression toward the testis, with much lower expression in other tissues.[15]

Expression of C16orf78 across multiple human tissues[16]

Interaction

C16orf78 has a physical association with DNA/RNA-binding protein KIN17 (NP_036443.1), suggesting C16orf78 may also play a role in DNA repair.[17] C16orf78 was found to be phosphorylated by SRPK1(NP_003128.3) and SPRK2 (AAH68547.1).[6]

Clinical Significance

Deletion of the C16orf78 gene has been identified as a determinant of prostate cancer.[18] A SNP in C16orf78 interacts with a SNP in LMTK2 and is associated with risk of prostate cancer.[19]

Amplification of the C16orf78 gene has been linked to metabolically adaptive cancer cells.[20] A duplication of the C16orf78 gene was associated with at least one case of Rolandic Epilepsy.[21]

Homology

Paralogs

C16orf78 has no known paralogs in humans.[22]

Orthologs

C16orf78 has over 80 orthologs, including animals as distant Ciona intestinalis(XP_002132057.1), which is estimated to have diverged from humans 676 million years ago.[2][23] C16orf78 has orthologs in many types of mammals, reptiles, bony fish, and even some invertebrates, but has no known orthologs in amphibians or birds.[22] Below is a table with samples of orthologs, with divergence dates from TimeTree and similarity calculated by pairwise sequence alignment.[24]

Table of C16orf78 Orthologs
Species Name NCBI Accession Divergence (mya) (estimated) Length (aa) % Identity % Similarity
Homo sapiens NP_653203.1 0 265 100% 100%
Gorilla gorilla gorilla XP_004057673.2 9.06 265 96% 98%
Macaca mulatta XP_001082258.1 29.44 267 89% 93%
Galeopterus variegatus XP_008591134.1 76 266 65% 77%
Oryctolagus cuniculus XP_008273281.1 90 255 62% 76%
Mus musculus NP_808569.1 90 270 57% 69%
Lipotes vexillifer XP_007459548.1 96 266 65% 77%
Capra hircus XP_017918754.1 96 276 63% 74%
Callorhinus ursinus XP_025708226.1 96 250 62% 74%
Pteropus vampyrus XP_011358492.1 96 263 60% 74%
Loxodonta africana XP_023411324.1 105 285 48% 55%
Sarcophilus harrisii XP_003757266.1 159 270 38% 53%
Vombatus ursinus XP_027723426.1 159 275 38% 54%
Pogona vitticeps XP_020643996.1 312 315 26% 43%
Gekko japonicus XP_015263322.1 312 261 25% 47%
Python bivittatus XP_025030465.1 312 313 23% 37%
Latimeria chalumnae XP_014344069.1 413 310 19% 42%
Acipenser ruthenus RXM34621.1 435 202 15% 37%
Ciona intestinalis XP_002132057.1 676 396 10% 32%
Apostichopus japonicus PIK46940.1 684 292 9% 33%

References

  1. ↑ "uncharacterized protein C16orf78 [Homo sapiens - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/NP_653203.1. 
  2. ↑ 2.0 2.1 2.2 "Gene: C16orf78 (ENSG00000166152) - Summary - Homo sapiens - Ensembl genome browser 96". http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000166152;r=16:49373823-49399431;t=ENST00000299191. 
  3. ↑ "ExPASy - ProtParam tool". https://web.expasy.org/protparam/. 
  4. ↑ "SAPS < Sequence Statistics < EMBL-EBI". https://www.ebi.ac.uk/Tools/seqstats/saps/. 
  5. ↑ Schindeldecker, Mario; Moosmann, Bernd (10 April 2015). "Protein-borne methionine residues as structural antioxidants in mitochondria". Amino Acids 47 (7): 1421–1432. doi:10.1007/s00726-015-1955-8. PMID 25859649. 
  6. ↑ 6.0 6.1 "C16orf78 Result Summary | BioGRID". https://thebiogrid.org/125845/summary/homo-sapiens/c16orf78.html. 
  7. ↑ "C16orf78 (human)". https://www.phosphosite.org/proteinAction?id=16329&showAllSites=true. 
  8. ↑ "PROSITE". https://prosite.expasy.org/cgi-bin/prosite/mydomains/. 
  9. ↑ "CFSSP: Chou & Fasman Secondary Structure Prediction Server". http://www.biogem.org/tool/chou-fasman/. 
  10. ↑ "NPS@ : GOR4 secondary structure prediction". https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html. 
  11. ↑ "JPred: A Protein Secondary Structure Prediction Server" (in en). http://www.compbio.dundee.ac.uk/jpred/. 
  12. ↑ Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael J E (7 May 2015). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols 10 (6): 845–858. doi:10.1038/nprot.2015.053. PMID 25950237. 
  13. ↑ Horton, P.; Park, K.-J.; Obayashi, T.; Fujita, N.; Harada, H.; Adams-Collier, C.J.; Nakai, K. (8 May 2007). "WoLF PSORT: protein localization predictor". Nucleic Acids Research 35 (Web Server): W585–W587. doi:10.1093/nar/gkm259. PMID 17517783. 
  14. ↑ "Motif Scan" (in en). https://myhits.isb-sib.ch/cgi-bin/motif_scan. 
  15. ↑ "C16orf78 chromosome 16 open reading frame 78 [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&list_uids=123970#gene-expression. 
  16. ↑ "49000288 - GEO Profiles - NCBI". https://www.ncbi.nlm.nih.gov/geoprofiles/49000288. 
  17. ↑ IntAct. "IntAct Portal" (in en). https://www.ebi.ac.uk/intact/interaction/EBI-20903736. 
  18. ↑ DePihno, R. A et al. (2016). U.S. Patent No. 9458510. Washington, DC: U.S. Patent and Trademark Office.
  19. ↑ Tao, Sha; Wang, Zhong; Feng, Junjie; Hsu, Fang-Chi; Jin, Guangfu; Kim, Seong-Tae; Zhang, Zheng; Gronberg, Henrik et al. (March 2012). "A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants". Carcinogenesis 33 (3): 598–603. doi:10.1093/carcin/bgr316. PMID 22219177. 
  20. ↑ Singh, Balraj; Shamsnia, Anna; Raythatha, Milan R.; Milligan, Ryan D.; Cady, Amanda M.; Madan, Simran; Lucci, Anthony; Das, Gokul M. (3 October 2014). "Highly Adaptable Triple-Negative Breast Cancer Cells as a Functional Model for Testing Anticancer Agents". PLOS ONE 9 (10): e109487. doi:10.1371/journal.pone.0109487. PMID 25279830. Bibcode: 2014PLoSO...9j9487S. 
  21. ↑ Reinthaler, Eva M.; Lal, Dennis; Lebon, Sebastien; Hildebrand, Michael S.; Dahl, Hans-Henrik M.; Regan, Brigid M.; Feucht, Martha; Steinböck, Hannelore et al. (15 November 2014). "16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy". Human Molecular Genetics 23 (22): 6069–6080. doi:10.1093/hmg/ddu306. PMID 24939913. 
  22. ↑ 22.0 22.1 "BLAST: Basic Local Alignment Search Tool". https://blast.ncbi.nlm.nih.gov/Blast.cgi. 
  23. ↑ "TimeTree :: The Timescale of Life". http://www.timetree.org/. 
  24. ↑ "Pairwise Sequence Alignment Tools < EMBL-EBI". https://www.ebi.ac.uk/Tools/psa/. 

External links



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