Biology:C20orf202

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C20orf202
File:Ideogram human chromosome 20.svg
Chromosome 20
Identifiers
SymbolC20orf202
NCBI gene400831
HGNC37254
RefSeqNM_001009612.3
UniProtA1L168

C20orf202 (chromosome 20 open reading frame 202) is a protein that in humans is encoded by the C20orf202 gene. In humans, this gene encodes for a nuclear protein that is primarily expressed in the lung and placenta.[1]

Gene

C20orf202 is located on the plus strand of chromosome 20 at 20p13.[2] The gene is 4,826 base pairs long. It spans from chr20:1,184,098-1,188,918, and contains 2 exons.[3]

Transcript

There is one transcript of C20orf202. The mRNA sequence is 1,609 base pairs long.[4]

Protein

The protein encoded by C20orf202 is 122 amino acids in length with a predicted molecular mass of 13591 Da and a predicted isoelectric point of 9.13 pl/MW.[5][6] C20orf202 contains PFAM domain DUF3461 at amino acids 3-67.[7] This domain codes for a protein of unknown function. The structure of C20orf202 consists of 46.72% random coils, 42.62% alpha helixes, and 10.66% extended strands.[8]

C20orf202 quartenary structure[9]

Regulation

Gene level regulation

C20orf202 transcription binding factor sites in the promoter

The C20orf202 promoter has many transcription factor binding sites, most notably at the beginning and end of the promoter. These sites are shown in the figure to the right and are listed below with their respective functions.[10]

C20orf202 transcription binding factor sites

Transcript level regulation

MicroRNA binding sites are only found in the 3' UTR of C20orf202. Most of these sites are found in the beginning or end of the 3' UTR, with many located in close proximity to each other.[11] These 3' UTR microRNA binding sites can be seen in the figure to the right.

C20orf202 3' UTR microRNA binding sites

Protein level regulation

C20orf202 has many phosphorylation and glycosylation sites throughout the protein.[12][13] A few of the phosphorylation sites are located in highly conserved regions of the protein.

Expression

In humans, C20orf202 has moderate mRNA abundance across cells types, though higher than average expression in the kidney and heart, it is not significantly so.[14] Additionally C20orf202 expression increases during fetal development of kidney, lung, and intestinal tissues.[15]

C20orf202 expression profile via NCBI GEO GDS3113. The graph shows expression levels of C20orf202 within various normal tissues within humans. The most notable higher expression levels are in the kidney and the heart, however not significantly so. Red bars indicate the absolute expression levels and blue dots are the percentile rank of gene expression within the sample.[16]

Homology

Paralogs

C20orf202 has three known paralogs- FAM167a, FAM167b, and AARD.[17]

C20orf202 paralog phylogeny[18]

Orthologs

C20orf202 orthologs can be found in major groups such as mammals, reptiles, amphibians, and distantly fish.

This table lists several orthologs for C20orf202 including genus and species, common name, taxonomic group, evolutionary date of divergence, accession number, sequence length, sequence identity, and sequence similarity.

C20orf202 orthologs
Genus and species Common name Taxonomic group Estimated date of divergence Accession number Length (amino acids) Sequence identity Sequence similarity
Homo sapiens Human Mammalia (Primata) 0 NP_001009612.1 122 100% 100%
Pan troglodytes Chimpanzee Mammalia (Primata) 6.7 XP_001167776.1 122 99% 99%
Dipodomys ordii Ord's kangaroo rat Mammalia (Rodentia) 90 XP_012866108.1 151 74% 87%
Peromyscus maniculatus Deer mouse Mammalia (Rodentia) 90 XP_006985608.1 192 68% 81%
Fukomys damarensis Damaraland mole-rat Mammalia (Rodentia) 90 XP_010611217.1 131 67% 77%
Grammomys surdaster African woodland thicket rat Mammalia (Rodentia) 90 XP_028630806.1 190 60% 71%
Sus scrofa Wild boar Mammalia (Artiodactyla) 96 XP_013840663.1 123 84% 90%
Monodon monoceros Narwhal Mammalia (Artiodactyla) 96 XP_029077716.1 153 79% 90%
Delphinapterus leucas Beluga whale Mammalia (Artiodactyla) 96 XP_022448507.1 153 79% 90%
Orcinus orca Orca Mammalia (Artiodactyla) 96 XP_004273009.1 136 78% 90%
Eptesicus fuscus Big brown bat Mammalia (Chiroptera) 96 XP_028000906.1 179 79% 88%
Vulpes vulpes Red fox Mammalia (Carnivora) 96 XP_025841919.1 163 79% 88%
Canis lupus familiaris Dog Mammalia (Carnivora) 96 XP_022265199.1 125 77% 87%
Lacerta agilis Sand lizard Reptilia (Squamata) 312 XP_033006940.1 95 47% 64%
Podarcis muralis Common wall lizard Reptilia (Squamata) 312 XP_028591365.1 95 45% 58%
Chelonoidis abingdonii Pinta Island tortoise Reptilia (Testudines) 312 XP_032622241.1 98 46% 61%
Alligator sinensis Chinese alligator Reptilia (Crocodilia) 312 XP_006030613.1 98 42% 59%
Nanorana parkeri High Himalaya frog Amphibia (Anura) 351.8 XP_018411922.1 114 44% 58%
Cyprinodon variegatus Sheepshead minnow Actinopterygii (Cyprinodontiformes) 435 XP_015232405.1 146 54% 72%
Cyprinus carpio Common carp Actinopterygii (Cyprinodontiformes) 435 KTF83963.1 190 47% 68%

Interacting proteins

Two hybrid prey pooling followed by two hybrid array revealed that C20orf202 is predicted to interact with two other proteins: SNAPAP and HNRNPCL1.[19] SNAPAP (SNARE-associated protein) has a role in the SNARE binding complex, and is also associated with Hermansky–Pudlak syndrome and tricuspid valve stenosis.[20] HNRNPCL1 (Heterogeneous Nuclear Ribonucleoprotein C Like 1) has a role in RNA binding and nucleosome assembly.[21]

Clinical significance

C20orf202 has been associated by GWAS to multiple sclerosis.[22] Additionally, through in silico analysis, C20orf202 was identified as being involved in chromosome 20p inv dup del syndrome, a syndrome similar to trisomy 20p.[23]

References

  1. ↑ "C20orf202 chromosome 20 open reading frame 202 [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene/?term=Homo+sapiens+C20orf202. 
  2. ↑ "uncharacterized protein C20orf202 [Homo sapiens - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/NP_001009612.1. 
  3. ↑ "C20orf202 chromosome 20 open reading frame 202 [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene/?term=Homo+sapiens+C20orf202. 
  4. ↑ "Homo sapiens chromosome 20 open reading frame 202 (C20orf202), mRNA". 26 October 2019. https://www.ncbi.nlm.nih.gov/nuccore/NM_001009612.3. 
  5. ↑ "ExPASy - Compute pI/Mw tool". https://web.expasy.org/compute_pi/. 
  6. ↑ "C20orf202 Gene - GeneCards | CT202 Protein | CT202 Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=C20orf202. 
  7. ↑ "MOTIF: Searching Protein Sequence Motifs". https://www.genome.jp/tools/motif/. 
  8. ↑ "NPS@ : GOR4 secondary structure prediction". https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html. 
  9. ↑ "I-TASSER server for protein structure and function prediction". https://zhanglab.ccmb.med.umich.edu/I-TASSER/. 
  10. ↑ "Genomatix: Genome Annotation and Browser: Query Input". https://www.genomatix.de/cgi-bin/eldorado/eldorado.pl?s=5c294c68e017fe50c749ada37b9936c9. 
  11. ↑ "miRDB - MicroRNA Target Prediction Database". http://mirdb.org/cgi-bin/search.cgi. 
  12. ↑ "NetPhos 3.1 Server". http://www.cbs.dtu.dk/services/NetPhos/. 
  13. ↑ "NetGlycate 1.0 Server" (in en). http://www.cbs.dtu.dk/services/NetGlycate/. 
  14. ↑ "GDS3113 / 228292". https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS3113:228292. 
  15. ↑ "C20orf202 chromosome 20 open reading frame 202 [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=400831. 
  16. ↑ "GDS3113 / 228292". https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS3113:228292. 
  17. ↑ "C20orf202 Gene - GeneCards | CT202 Protein | CT202 Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=C20orf202. 
  18. ↑ "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". https://www.ebi.ac.uk/Tools/msa/clustalo/. 
  19. ↑ "C20orf202 protein (human) - STRING interaction network". https://string-db.org/cgi/network.pl?taskId=CA5MNIxHPRuS. 
  20. ↑ "SNAPIN Gene - GeneCards | SNAPN Protein | SNAPN Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=SNAPIN. 
  21. ↑ "HNRNPCL1 Gene - GeneCards | HNRC1 Protein | HNRC1 Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=HNRNPCL1. 
  22. ↑ "GWAS Catalog". https://www.ebi.ac.uk/gwas/variants/rs397020. 
  23. ↑ "Chromosome 20p inverted duplication deletion identified in a Thai female adult with mental retardation, obesity, chronic kidney disease and characteristic facial features". European Journal of Medical Genetics 56 (6): 319–24. June 2013. doi:10.1016/j.ejmg.2013.03.011. PMID 23542666. 



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