Jump to content

User:Brandon485673/sandbox

From Wikipedia, the free encyclopedia

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

[edit]

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

mRNA

[edit]

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

[edit]

Sequence

[edit]

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

[edit]

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

[edit]

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

[edit]

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

Expression

[edit]

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

Expression of C16orf78 across multiple human tissues[16]

Interaction

[edit]

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

[edit]

Deletion of the C16orf78 gene has been identified as a determinant of prostate cancer.[18] A SNP in C16orf78 interacts with 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

[edit]

Paralogs

[edit]

C16orf78 has no known paralogs in humans.[22]

Orthologs

[edit]

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

[edit]
  1. ^ "uncharacterized protein C16orf78 [Homo sapiens] - Protein - NCBI". www.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". www.ebi.ac.uk. Retrieved 2019-05-05.
  5. ^ Schindeldecker, Mario; Moosmann, Bernd (2015-7). "Protein-borne methionine residues as structural antioxidants in mitochondria". Amino Acids. 47 (7): 1421–1432. doi:10.1007/s00726-015-1955-8. ISSN 0939-4451. {{cite journal}}: Check date values in: |date= (help)
  6. ^ a b "C16orf78 Result Summary | BioGRID". thebiogrid.org. Retrieved 2019-05-05.
  7. ^ "C16orf78 (human)". www.phosphosite.org. Retrieved 2019-05-05.
  8. ^ "PROSITE". prosite.expasy.org. Retrieved 2019-05-05.
  9. ^ "CFSSP: Chou & Fasman Secondary Structure Prediction Server". www.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". www.compbio.dundee.ac.uk. Retrieved 2019-05-05.
  12. ^ Sternberg, Michael J. E.; Wass, Mark N.; Yates, Christopher M.; Mezulis, Stefans; Kelley, Lawrence A. (2015-06). "The Phyre2 web portal for protein modeling, prediction and analysis". Nature Protocols. 10 (6): 845–858. doi:10.1038/nprot.2015.053. ISSN 1750-2799. {{cite journal}}: Check date values in: |date= (help)
  13. ^ Horton, Paul; Park, Keun-Joon; Obayashi, Takeshi; Fujita, Naoya; Harada, Hajime; Adams-Collier, C. J.; Nakai, Kenta (2007-7). "WoLF PSORT: protein localization predictor". Nucleic Acids Research. 35 (Web Server issue): W585–587. doi:10.1093/nar/gkm259. ISSN 1362-4962. PMC PMCPMC1933216. PMID 17517783. {{cite journal}}: Check |pmc= value (help); Check date values in: |date= (help)
  14. ^ "Motif Scan". myhits.isb-sib.ch. Retrieved 2019-05-05.
  15. ^ "C16orf78 chromosome 16 open reading frame 78 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-05-05.
  16. ^ "49000288 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2019-05-05.
  17. ^ IntAct. "https://www.ebi.ac.uk/intact/interaction/EBI-20903736". www.ebi.ac.uk. Retrieved 2019-05-05. {{cite web}}: External link in |title= (help)
  18. ^ DePihno, R. A et. al. (2016). U.S. Patent No. 9458510. Washington, DC: U.S. Patent and Trademark Office.
  19. ^ Sun, Jielin; Xu, Jianfeng; Isaacs, William B.; Zheng, Lilly S.; Gronberg, Henrik; Zhang, Zheng; Kim, Seong-Tae; Jin, Guangfu; Hsu, Fang-Chi (2012-03-01). "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. ISSN 0143-3334. PMC 3291863. PMID 22219177.{{cite journal}}: CS1 maint: PMC format (link)
  20. ^ Singh, Balraj; Shamsnia, Anna; Raythatha, Milan R.; Milligan, Ryan D.; Cady, Amanda M.; Madan, Simran; Lucci, Anthony (2014-10-03). Das, Gokul M. (ed.). "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. ISSN 1932-6203. PMC 4184880. PMID 25279830.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  21. ^ Neubauer, Bernd A.; Zimprich, Fritz; Reymond, Alexandre; Jacquemont, Sebastien; Sander, Thomas; Beckmann, Jacques S.; Berkovic, Samuel F.; Scheffer, Ingrid E.; Mefford, Heather (2014-11-15). "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. ISSN 0964-6906.
  22. ^ a b "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2019-05-05.
  23. ^ "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2019-05-05.
  24. ^ "Pairwise Sequence Alignment Tools < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-05-05.
[edit]
Retrieved from "https://en.wikipedia.org/w/index.php?title=User:Brandon485673/sandbox&oldid=895682239"