Biology:C16orf46

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Short description: Human gene


A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example


3D Rendering of C16orf46.[1]

Chromosome 16 open reading frame 46 is a protein of yet to be determined function in Homo sapiens. It is encoded by the C16orf46 gene with NCBI accession number of NM_001100873. It is a protein-coding gene with an overlapping locus.[2]

Gene

An alternative name for this gene is FLJ32702, however it is most commonly referred to as C16orf46.[3]

Location

The C16orf26 gene is found on chromosome 16q23.2 negative strand.[4] The promoter region is 1152 base pairs long.[5] It has three exons, one from 1-380 bp, the second from 381 to 1254 bp, and the third from 1255 to 1982 bp.[2]

Expression

C16orf46 is broadly expressed in the testis and thyroid as well as 18 other tissues.[4] These tissue expression patterns are found to be low to moderate (25-50%).[6] When looking at tissue profiles, the highest expression is in the adult mammalian kidney, liver, prefrontal cortex, cerebellum, heart, and brain.[7]

Protein

Immunofluorescence for C16orf46 in a rabbit.[8]

Protein Analysis

The full C16orf46 protein is 417 amino acids long.[9] It has no isoforms, and its most distant ortholog, Rhincodon typus (whale shark), also has no known isoforms.[10] The molecular weight was found to be 45.8 kdal.[11] The isoelectric point is 7.4, average for all proteins, and C16orf46 is electrically neutral.[12]

C16orf46 is predicted to be found in the nucleus by all orthologs.[13]

The secondary structure of C16orf46 has alternating alpha helices and beta sheets.[14]

Protein Level Regulation

In C16orf46, there is N-linked glycosylation, O-linked glycosylation, and SUMOylation.[15][16]

There are phosphorylation sites found with the kinases CKII, CKI, PKC, and cdc2.[17]

A coronavirus cleavage site is predicted at the 235 amino acid position.[18] There are also tyrosine motif locations between amino acids 42-45 and 251–252.[19]

Transcript Level Regulation

mRNA folding on the 5' UTR predicts a stem loop twice in the area between base pairs 47–90.[20]

Homologs

Orthologs

C16orf46 has over 50 orthologs ranging from primate to chordate.[21] The table below shows a representation of the diversity of C16orf46 by listing a selection of orthologs found using NCBI. When C16orf46 Homo sapiens was run through a multiple alignment sequence program, Clustal Omega, against 20 true orthologs and 16 distant orthologs, Trp74 and Pro212 were found to be conserved in all.[22]

Species Common Name Divergence (MYA) Accession Number Identity
Homo sapiens Humans --- XP_016878405.1 100.0%
Ochotona princeps American Pika 90 XP_004584265.1 52.7%
Octodon degus Common Degu 90 XP_003434773.2 47.8%
Ursus maritimus Polar Bear 96 XP_008687958.1 67.5%
Leptonychotes weddellii Weddell Seal 96 XP_006748170.1 67.2%
Canis lupus Gray Wolf 96 XP_003434773.2 65.8%
Pteropus vampyrus Large Flying Fox 96 XP_011354946.1 63.5%
Sus scrofa Wild Boar 96 XP_020952705.1 61.5%
Bos indicus Zebu 96 XP_019835282.1 60.2%
Erinaceus europaeus European Hedgehog 96 XP_007516703.1 56.7%
Loxodonta africana African Bush Elephant 105 XP_010596137.1 60.9%
Sarcophilus harrisii Tasmanian Devil 159 XP_003757901.1 43.1%
Apteryx australis Southern Brown Kiwi 312 XP_013796688.1 18.5%
Aptenodytes forsteri Emperor Penguin 312 XP_019327074.1 17.4%
Chelonia mydas Green Sea Turtle 312 XP_007059324.1 29.7%
Gekko japonicus Gekko Japonicus 312 XP_015261305.1 25.3%
Nanorana parkeri High Himalaya Frog 352 XP_018410908.1 22.4%
Pygocentrus nattereri Red Bellied Piranha 435 XP_017578196.1 21.2%
Lepisosteus oculatus Spotted Gar 435 XP_015223705.1 20.6%
Callorhinchus milii Australian Ghost Shark 473 XP_007887408.1 22.7%

Paralogs

C16orf46 has no known paralogs.[21]

Mutations

C16orf46 has been compared against Fibrinogen, a protein which mutates rapidly, and Cytochrome C, a protein which mutates slowly.

As can be seen below, when multiple species of the three proteins were plotted, C16orf46 more closely resembled that of Fibrinogen than Cytochrome C, suggesting a possible rapid mutation.[21]

The trend of C16orf46, as compared to Fibrinogen and Cytochrome C, suggests faster mutation rates as it diverges from Homo sapiens.

Interacting Proteins

C16orf46 interacts with FAT3 which has been linked to neurite interactions during development.[23] C16orf46 is thought to have coexpression with the PLAC8L1 and CFAP43 gene, both of unknown function.[24]

Clinical Significance

There are higher levels of C16orf46 expression in pancreatic adenocarcinoma tumor epithelia tissue compared to the control.[25] There is also higher gene expression in patients with small-cell carcinoma compared to the control.[26]

References

  1. ↑ "I-TASSER results". https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S395210/. [yes|permanent dead link|dead link}}]
  2. ↑ 2.0 2.1 "Gene: C16orf46 (OTTHUMG00000137629) - Summary - Homo sapiens - Vega Genome Browser 68" (in en-gb). http://vega.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=OTTHUMG00000137629;r=16:8105349. 
  3. ↑ Database, GeneCards Human Gene. "C16orf46 Gene - GeneCards | CP046 Protein | CP046 Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=C16orf46. 
  4. ↑ 4.0 4.1 "C16orf46 Symbol Report | HUGO Gene Nomenclature Committee". https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:26525. 
  5. ↑ "Genomatix - NGS Data Analysis & Personalized Medicine". https://www.genomatix.de/. 
  6. ↑ geo. "Home - GEO - NCBI" (in en). https://www.ncbi.nlm.nih.gov/geo/. 
  7. ↑ "Gene: C16orf46 - ENSG00000166455" (in en). https://bgee.org/?page=gene&gene_id=ENSG00000166455. 
  8. ↑ "Anti-C16orf46 antibody produced in rabbit HPA041136". https://www.sigmaaldrich.com/catalog/product/sigma/hpa041136?lang=en&region=US. 
  9. ↑ "uncharacterized protein C16orf46 isoform X1 [Homo sapiens - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/XP_016878406.1. 
  10. ↑ "uncharacterized protein C16orf46 homolog [Rhincodon typus - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/1160128351. 
  11. ↑ Kozlowski, Lukasz P.. "CALCULATION OF PROTEIN ISOELECTRIC POINT" (in en). http://isoelectric.org/calculate.php. 
  12. ↑ EMBL-EBI. "SAPS < Sequence Statistics < EMBL-EBI" (in en). https://www.ebi.ac.uk/Tools/seqstats/saps/. 
  13. ↑ "PSORT WWW Server". https://psort.hgc.jp/. 
  14. ↑ "Bioinformatics Toolkit". https://toolkit.tuebingen.mpg.de/#/jobs/3627327. 
  15. ↑ "NetNGlyc 1.0 Server" (in en). http://www.cbs.dtu.dk/services/NetNGlyc/. 
  16. ↑ "NetOGlyc 4.0 Server" (in en). http://www.cbs.dtu.dk/services/NetOGlyc/. 
  17. ↑ "NetPhos 3.1 Server" (in en). http://www.cbs.dtu.dk/services/NetPhos/. 
  18. ↑ "NetCorona 1.0 Server" (in en). http://www.cbs.dtu.dk/services/NetCorona/. 
  19. ↑ "Human Protein Reference Database". http://www.hprd.org/. 
  20. ↑ "The Mfold Web Server | mfold.rit.albany.edu" (in en). http://unafold.rna.albany.edu/?q=mfold. 
  21. ↑ 21.0 21.1 21.2 "BLAST: Basic Local Alignment Search Tool". https://blast.ncbi.nlm.nih.gov/Blast.cgi. 
  22. ↑ EMBL-EBI. "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI" (in en). https://www.ebi.ac.uk/Tools/msa/clustalo/. 
  23. ↑ Lab, Mike Tyers. "BioGRID | Database of Protein, Chemical, and Genetic Interactions" (in en). https://thebiogrid.org/. 
  24. ↑ "C16orf46 protein (human) - STRING interaction network" (in en). https://string-db.org/cgi/network.pl?taskId=Tsisxb0h6voQ. 
  25. ↑ "GDS4103 / 230281_at". https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS4103:230281_at. 
  26. ↑ "GDS4794 / 230281_at". https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS4794:230281_at. 



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