C16orf78

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

Contents

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. C16orf78Diagram.png
Diagram of C16orf78 protein with ubiquitination sites marked in red and phosphorylation sites marked in gray.

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. C16orf78Phyre2WikiShot.png
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 C16orf78 Tissue Expression Profile Graph.png
Expression of C16orf78 across multiple human tissues

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 NameNCBI 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%

References

  1. ↑ "uncharacterized protein C16orf78 [Homo sapiens] - Protein - NCBI". ncbi.nlm.nih.gov. Retrieved 2019-02-26.
  2. 1 2 3 "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. 1 2 "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. Archived from the original on 2019-04-02. 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. 1 2 "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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