C16orf78 Explained

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.

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]

Structure

Predictions of C16orf78's secondary structure consist primarily of alpha helices and coiled coils.[8] [9] [10] 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.[11]

Subcellular Localization

C16orf78 is predicted to be localized to the cell nucleus.[12] There is also a predicted bipartite nuclear localization signal.[13]

Expression

C16orf78 has restricted expression toward the testis, with much lower expression in other tissues.[14]

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.[15] C16orf78 was found to be phosphorylated by SRPK1(NP_003128.3) and SPRK2 (AAH68547.1).

Clinical Significance

Deletion of the C16orf78 gene has been identified as a determinant of prostate cancer.[16] A SNP in C16orf78 interacts with a SNP in LMTK2 and is associated with risk of prostate cancer.[17]

Amplification of the C16orf78 gene has been linked to metabolically adaptive cancer cells.[18] A duplication of the C16orf78 gene was associated with at least one case of Rolandic Epilepsy.[19]

Homology

Paralogs

C16orf78 has no known paralogs in humans.[20]

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.[21] C16orf78 has orthologs in many types of mammals, reptiles, bony fish, and even some invertebrates, but has no known orthologs in amphibians or birds. Below is a table with samples of orthologs, with divergence dates from TimeTree and similarity calculated by pairwise sequence alignment.[22]

Species Name
NCBI AccessionDivergence (mya) (estimated)Length (aa)% Identity% Similarity
Homo sapiensNP_653203.10265100%100%
Gorilla gorilla gorillaXP_004057673.29.0626596%98%
Macaca mulattaXP_001082258.129.4426789%93%
Galeopterus variegatusXP_008591134.17626665%77%
Oryctolagus cuniculusXP_008273281.19025562%76%
Mus musculusNP_808569.19027057%69%
Lipotes vexilliferXP_007459548.19626665%77%
Capra hircusXP_017918754.19627663%74%
Callorhinus ursinusXP_025708226.19625062%74%
Pteropus vampyrusXP_011358492.19626360%74%
Loxodonta africanaXP_023411324.110528548%55%
Sarcophilus harrisiiXP_003757266.115927038%53%
Vombatus ursinusXP_027723426.115927538%54%
Pogona vitticepsXP_020643996.131231526%43%
Gekko japonicusXP_015263322.131226125%47%
Python bivittatusXP_025030465.131231323%37%
Latimeria chalumnaeXP_014344069.141331019%42%
Acipenser ruthenusRXM34621.143520215%37%
Ciona intestinalisXP_002132057.167639610%32%
Apostichopus japonicusPIK46940.16842929%33%

Notes and References

  1. Web site: uncharacterized protein C16orf78 [Homo sapiens] - Protein - NCBI]. ncbi.nlm.nih.gov. 2019-02-26.
  2. Web site: Gene: C16orf78 (ENSG00000166152) - Summary - Homo sapiens - Ensembl genome browser 96. useast.ensembl.org. 2019-05-05.
  3. Web site: ExPASy - ProtParam tool. web.expasy.org. 2019-05-05.
  4. Web site: SAPS < Sequence Statistics < EMBL-EBI. ebi.ac.uk. 2019-05-05.
  5. Schindeldecker . Mario . Moosmann . Bernd . Protein-borne methionine residues as structural antioxidants in mitochondria . Amino Acids . 10 April 2015 . 47 . 7 . 1421–1432 . 10.1007/s00726-015-1955-8 . 25859649 . 16953847 .
  6. Web site: C16orf78 Result Summary BioGRID. thebiogrid.org. 2019-05-05.
  7. Web site: C16orf78 (human). phosphosite.org. 2019-05-05.
  8. Web site: CFSSP: Chou & Fasman Secondary Structure Prediction Server. biogem.org. 2019-05-05.
  9. Web site: NPS@ : GOR4 secondary structure prediction. npsa-prabi.ibcp.fr. 2019-05-05.
  10. Web site: JPred: A Protein Secondary Structure Prediction Server. compbio.dundee.ac.uk. en. 2019-05-05.
  11. Kelley . Lawrence A . Mezulis . Stefans . Yates . Christopher M . Wass . Mark N . Sternberg . Michael J E . The Phyre2 web portal for protein modeling, prediction and analysis . Nature Protocols . 7 May 2015 . 10 . 6 . 845–858 . 10.1038/nprot.2015.053 . 25950237 . 5298202 .
  12. Horton . P. . Park . K.-J. . Obayashi . T. . Fujita . N. . Harada . H. . Adams-Collier . C.J. . Nakai . K. . WoLF PSORT: protein localization predictor . Nucleic Acids Research . 8 May 2007 . 35 . Web Server . W585–W587 . 10.1093/nar/gkm259 . 1933216 . 17517783 .
  13. Web site: Motif Scan. myhits.isb-sib.ch. en. 2019-05-05.
  14. Web site: C16orf78 chromosome 16 open reading frame 78 [Homo sapiens (human)] - Gene - NCBI]. ncbi.nlm.nih.gov. 2019-05-05.
  15. Web site: IntAct Portal . IntAct. ebi.ac.uk. en. 2019-05-05.
  16. DePihno, R. A et al. (2016). U.S. Patent No. 9458510. Washington, DC: U.S. Patent and Trademark Office.
  17. Tao . Sha . Wang . Zhong . Feng . Junjie . Hsu . Fang-Chi . Jin . Guangfu . Kim . Seong-Tae . Zhang . Zheng . Gronberg . Henrik . Zheng . Lilly S. . Isaacs . William B. . Xu . Jianfeng . Sun . Jielin . A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants . Carcinogenesis . March 2012 . 33 . 3 . 598–603 . 10.1093/carcin/bgr316 . 3291863 . 22219177 .
  18. Singh . Balraj . Shamsnia . Anna . Raythatha . Milan R. . Milligan . Ryan D. . Cady . Amanda M. . Madan . Simran . Lucci . Anthony . Das . Gokul M. . Highly Adaptable Triple-Negative Breast Cancer Cells as a Functional Model for Testing Anticancer Agents . PLOS ONE . 3 October 2014 . 9 . 10 . e109487 . 10.1371/journal.pone.0109487 . 4184880 . 25279830 . 2014PLoSO...9j9487S . free .
  19. Reinthaler . Eva M. . Lal . Dennis . Lebon . Sebastien . Hildebrand . Michael S. . Dahl . Hans-Henrik M. . Regan . Brigid M. . Feucht . Martha . Steinböck . Hannelore . Neophytou . Birgit . Ronen . Gabriel M. . Roche . Laurian . Gruber-Sedlmayr . Ursula . Geldner . Julia . Haberlandt . Edda . Hoffmann . Per . Herms . Stefan . Gieger . Christian . Waldenberger . Melanie . Franke . Andre . Wittig . Michael . Schoch . Susanne . Becker . Albert J. . Hahn . Andreas . Männik . Katrin . Toliat . Mohammad R. . Winterer . Georg . Lerche . Holger . Nürnberg . Peter . Mefford . Heather . Scheffer . Ingrid E. . Berkovic . Samuel F. . Beckmann . Jacques S. . Sander . Thomas . Jacquemont . Sebastien . Reymond . Alexandre . Zimprich . Fritz . Neubauer . Bernd A. . Reinthaler . Eva M. . Zimprich . Fritz . Feucht . Martha . Steinböck . Hannelore . Neophytou . Birgit . Geldner . Julia . Gruber-Sedlmayr . Ursula . Haberlandt . Edda . Ronen . Gabriel M. . Roche . Laurian . Lal . Dennis . Nürnberg . Peter . Sander . Thomas . Lerche . Holger . Neubauer . Bernd . Zimprich . Fritz . Mörzinger . Martina . Feucht . Martha . Suls . Arvid . Weckhuysen . Sarah . Claes . Lieve . Deprez . Liesbet . Smets . Katrien . Van Dyck . Tine . Deconinck . Tine . De Jonghe . Peter . Møller . Rikke S . Klitten . Laura L. . Hjalgrim . Helle . Møller . Rikke S . Campus . Kiel . Helbig . Ingo . Muhle . Hiltrud . Ostertag . Philipp . von Spiczak . Sarah . Stephani . Ulrich . Nürnberg . Peter . Sander . Thomas . Trucks . Holger . Elger . Christian E. . Kleefuß-Lie . Ailing A. . Kunz . Wolfram S. . Surges . Rainer . Gaus . Verena . Janz . Dieter . Sander . Thomas . Schmitz . Bettina . Rosenow . Felix . Klein . Karl Martin . Reif . Philipp S. . Oertel . Wolfgang H. . Hamer . Hajo M. . Becker . Felicitas . Weber . Yvonne . Lerche . Holger . Koeleman . Bobby P.C. . de Kovel . Carolien . Lindhout . Dick . Lindhout . Dick . Ameil . Agnès . Andrieux . Joris . Bouquillon . Sonia . Boute . Odile . de Flandre . Jeanne . Cuisset . Jean Marie . Cuvellier . Jean-Christophe . Salengro . Roger . David . Albert . de Vries . Bert . Delrue . Marie-Ange . Doco-Fenzy . Martine . Fernandez . Bridget A. . Heron . Delphine . Keren . Boris . Lebel . Robert . Leheup . Bruno . Lewis . Suzanne . Mencarelli . Maria Antonietta . Mignot . Cyril . Minet . Jean-Claude . Moerman . Alexandre . Morice-Picard . Fanny . Mucciolo . Mafalda . Ounap . Katrin . Pasquier . Laurent . Petit . Florence . Ragona . Francesca . Rajcan-Separovic . Evica . Renieri . Alessandra . Rieubland . Claudine . Sanlaville . Damien . Sarrazin . Elisabeth . Shen . Yiping . van Haelst . Mieke . Silfhout . Anneke Vulto-van . 16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy . Human Molecular Genetics . 15 November 2014 . 23 . 22 . 6069–6080 . 10.1093/hmg/ddu306 . 24939913 . free .
  20. Web site: BLAST: Basic Local Alignment Search Tool. blast.ncbi.nlm.nih.gov. 2019-05-05.
  21. Web site: TimeTree :: The Timescale of Life. timetree.org. 2019-05-05.
  22. Web site: Pairwise Sequence Alignment Tools < EMBL-EBI. ebi.ac.uk. 2019-05-05.

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