Wikipedia

C16orf78

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

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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

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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

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Sequence

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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

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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

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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

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

Expression

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

 
Expression of C16orf78 across multiple human tissues[16]

Interaction

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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

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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

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Paralogs

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C16orf78 has no known paralogs in humans.[22]

Orthologs

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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

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  1. ^ "uncharacterized protein C16orf78 [Homo sapiens] - Protein - NCBI". ncbi.nlm.nih.gov. Retrieved 2019-02-26.
  2. ^ a b c "Gene: C16orf78 (ENSG00000166152) - Summary - Homo sapiens - Ensembl genome browser 96". useast.ensembl.org. Retrieved 2019-05-05.
  3. ^ "ExPASy - ProtParam tool". web.expasy.org. Retrieved 2019-05-05.
  4. ^ "SAPS < Sequence Statistics < EMBL-EBI". ebi.ac.uk. Retrieved 2019-05-05.
  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. S2CID 16953847.
  6. ^ a b "C16orf78 Result Summary | BioGRID". thebiogrid.org. Retrieved 2019-05-05.
  7. ^ "C16orf78 (human)". phosphosite.org. Retrieved 2019-05-05.
  8. ^ "PROSITE". prosite.expasy.org. Retrieved 2019-05-05.
  9. ^ "CFSSP: Chou & Fasman Secondary Structure Prediction Server". biogem.org. Retrieved 2019-05-05.
  10. ^ "NPS@ : GOR4 secondary structure prediction". npsa-prabi.ibcp.fr. Retrieved 2019-05-05.
  11. ^ "JPred: A Protein Secondary Structure Prediction Server". compbio.dundee.ac.uk. Retrieved 2019-05-05.
  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. PMC 5298202. 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. PMC 1933216. PMID 17517783.
  14. ^ "Motif Scan". myhits.isb-sib.ch. Retrieved 2019-05-05.
  15. ^ "C16orf78 chromosome 16 open reading frame 78 [Homo sapiens (human)] - Gene - NCBI". ncbi.nlm.nih.gov. Retrieved 2019-05-05.
  16. ^ "49000288 - GEO Profiles - NCBI". ncbi.nlm.nih.gov. Retrieved 2019-05-05.
  17. ^ IntAct. "IntAct Portal". ebi.ac.uk. Retrieved 2019-05-05.
  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; Zheng, Lilly S.; Isaacs, William B.; Xu, Jianfeng; Sun, Jielin (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. PMC 3291863. 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. Bibcode:2014PLoSO...9j9487S. doi:10.1371/journal.pone.0109487. PMC 4184880. PMID 25279830.
  21. ^ 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 (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. ^ a b "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2019-05-05.
  23. ^ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2019-05-05.
  24. ^ "Pairwise Sequence Alignment Tools < EMBL-EBI". ebi.ac.uk. Retrieved 2019-05-05.
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