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Draft:C3orf80

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C3orf80
Identifiers
AliasesC3orf80, chromosome 3 open reading frame 80
External IDsMGI: 1915975; HomoloGene: 110165; GeneCards: C3orf80; OMA:C3orf80 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

401097

68725

Ensembl

ENSG00000180044

ENSMUSG00000046999

UniProt

F5H4A9

E9Q0B3

RefSeq (mRNA)

NM_001168214

NM_001167996

RefSeq (protein)

NP_001161686

NP_001161468

Location (UCSC)Chr 3: 160.23 – 160.23 MbChr 3: 68.78 – 68.78 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Uncharacterized Membrane Protein C3orf80 (C3orf80) is a human protein encoded by the C3orf80 gene.[5]

Gene

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C3orf80 is on chromosome 3 from 160,225,422 to 160,228,213 bp.[6] It spans 2,792 bases on the plus strand and contains only one exon.[5]

Neighborhood

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Neighboring genes of C3orf80 include IFT80, BRD7P2, and SMC4.[5]

Gene Orientation Location Function
IFT80 Minus strand 160,256,986-160,399,880 Part of IFT complex B[7]
BRD7P2 Plus strand 160,100,691-160,102,912 Pseudogene of BRD7[8]
SMC4 Plus strand 160,399,274-160,434,954 Part of the condensin complex[9]

Transcript

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The mRNA transcript of human C3orf80 contains no introns, has only one isoform, and the complete sequence has been found.[5][10]

Expression

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PROTTER diagram of C3orf80[11]
Annotated AlphaFold model of C3orf80[12]

Expression of C3orf80 is highest in the cerebral cortex, esophagus, and colon.[13] A higher expression of C3orf80 has been observed from multiple sclerosis brain lesions.[14][15] Expression of C3orf80 has also been found by machine learning to be associated with different forms of cancer. A two-fold increase in expression was found in low-grade glioma based on whether the cells expressed CMTM3 or not.[16] A 107.61 fold increase in expression was seen after inhibition of CLIC1 in esophageal squamous cell carcinoma.[17] C3orf80 was one of three genes’ expression levels found to form the best machine learning model for predicting invasive carcinoma.[18] Finally, C3orf80 was one of 34 genes used in a machine learning model to predict if patients had a response to FOLFIRI chemotherapy.[19]

Protein

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C3orf80 is 247 amino acids long, has a molecular weight of 25.6 kDa before modifications, and has been proven to exist at the protein level, however, the tertiary structure is unknown.[6] The protein is annotated to be a single-pass membrane protein, localizing at the cell membrane.[20] The amino acid sequence of C3orf80 contains a signal peptide, transmembrane region, disordered region, glycosylation, and domain of unknown function 4719 (DUF4719).[20] The signal peptide is 35 amino acids long and is not part of the mature protein.

Graph showing corrected percent differences between orthologs and human genes over date of divergence.

Within humans, there is 0.02 ppm of C3orf80, a relatively low amount compared to other proteins.[21] Immunochemical staining has shown protein localization in cilia of glandular cells of the human fallopian tube.[22]

Evolution

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Orthologs

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Orthologs of human C3orf80 are specific to vertebrates.[23] The farthest ortholog of human C3orf80 is found in Callorhinchus milii, with a date of divergence of 462 million years ago.[24] Orthologs can be found in all major groups from Chondrichthyes to Mammalia; however, Aves have very unique orthologs of C3orf80 compared to any other group.[25][26] When comparing C3orf80 orthologs' rate of change in gene similarity over time to other proteins, C3orf80 is more similar to fibrinogen alpha chain, a quick evolving gene, compared to cytochrome C, a slow evolving gene.

Scientific Name Common Name Group Date of Divergence (mya)[27] Ortholog Accession Number Sequence Length Sequence Identity[28] Sequence Similarity[28]
Homo sapiens Human Mammalia 0 NP_001161686.1[5] 247 100% 100%
Mus musculus House mouse Mammalia 87 NP_001161468.1[29] 247 92% 94%
Antechinus flavipes Yellow-footed antechinus Marsupialia 160 XP_051839055.1[30] 237 59% 65%
Sarcophilus harrisii Tasmanian devil Marsupialia 160 XP_031813452.1[31] 239 58% 65%
Alligator mississippiensis American alligator Reptilia 319 XP_019347204.1[32] 210 54% 58%
Mauremys mutica Yellow pond turtle Reptilia 319 XP_044885017.1[33] 203 50% 54%
Prinia subflava Tawny-flanked prinia Aves 319 XP_063264524.1[34] 179 27% 33%
Gallus gallus Red junglefowl Aves 319 XP_025009399.2[35] 145 26% 31%
Aquila chrysaetos Golden eagle Aves 319 XP_029884193.1[36] 319 20% 25%
Pseudophryne corroboree Southern corroboree frog Amphibia 352 XP_063772225.1[37] 194 48% 54%
Bufo bufo Common toad Amphibia 352 XP_040286993.1[38] 189 46% 53%
Pleurodeles waltl Iberian ribbed newt Amphibia 352 KAJ1088024.1[39] 240 41% 47%
Rhinatrema bivittatum Rhinatrema Amphibia 352 XP_029473235.1[40] 206 41% 46%
Protopterus annectens West African lungfish Sarcopterygii 408 XP_043926856.1[41] 210 38% 44%
Latimeria chalumnae West Indian Ocean coelacanth Sarcopterygii 415 XP_006002129.1[42] 189 39% 44%
Polypterus senegalus Gray bichir Actinopterygii 429 XP_039612526.1[43] 196 34% 45%
Chelmon rostratus Copperband butterflyfish Actinopterygii 429 XP_041796725.1[44] 219 31% 42%
Danio rerio Zebrafish Actinopterygii 429 XP_068069764.1[45] 162 31% 39%
Stegostoma tigrinum Zebra shark Chondrichthyes 462 XP_048398267.1[46] 196 30% 40%
Callorhinchus milii Australian ghostshark Chondrichthyes 462 XP_007888000.1[47] 220 29% 35%

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000180044 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000046999 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c d e "C3orf80 chromosome 3 open reading frame 80 [Homo sapiens (human)]". Gene. U.S. National Center for Biotechnology Information (NCBI). Retrieved 2024-09-21.
  6. ^ a b "C3orf80". GeneCards. Retrieved 2024-09-20.
  7. ^ "IFT80". GeneCards. Retrieved 2024-12-04.
  8. ^ "BRD7P2". GeneCards. Retrieved 2024-12-04.
  9. ^ "SMC4". GeneCards. Retrieved 2024-12-04.
  10. ^ "Homo sapiens chromosome 3 open reading frame 80 (C3orf80), mRNA". Nucleotide Database. U.S. National Center for Biotechnology Information (NCBI). 26 February 2021. Retrieved 2024-09-21.
  11. ^ "Welcome to Protter". Protter - interactive protein feature visualization. Retrieved 2024-12-04.
  12. ^ "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk. Retrieved 2024-12-05.
  13. ^ "Tissue expression of C3orf80 - Summary - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2024-12-05.
  14. ^ Han MH, Lundgren DH, Jaiswal S, Chao M, Graham KL, Garris CS, et al. (2012-06-25). "Janus-like opposing roles of CD47 in autoimmune brain inflammation in humans and mice". Journal of Experimental Medicine. 209 (7): 1325–1334. doi:10.1084/jem.20101974. ISSN 0022-1007.
  15. ^ "90455088 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  16. ^ Li S, Gao P, Dai X, Ye L, Wang Z, Cheng H (February 2022). "New prognostic biomarker CMTM3 in low grade glioma and its immune infiltration". Annals of Translational Medicine. 10 (4): 206. doi:10.21037/atm-22-526. PMC 8908177. PMID 35280380.
  17. ^ Kobayashi T, Shiozaki A, Nako Y, Ichikawa D, Kosuga T, Shoda K, et al. (May 2018). "Chloride intracellular channel 1 as a switch among tumor behaviors in human esophageal squamous cell carcinoma". Oncotarget. 9 (33): 23237–23252. doi:10.18632/oncotarget.25296. PMC 5955400. PMID 29796185.
  18. ^ Wu Y, Min KY, Liu JF, Liang WF, Yang YH, Hu G, et al. (April 2024). "[Identification of Protein-Coding Gene Markers in Breast Invasive Carcinoma Based on Machine Learning]". Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae. 46 (2): 147–153. doi:10.3881/j.issn.1000-503X.15717. PMID 38686709.
  19. ^ Amniouel S, Jafri MS (2024-01-18). "High-accuracy prediction of colorectal cancer chemotherapy efficacy using machine learning applied to gene expression data". Frontiers in Physiology. 14: 1272206. doi:10.3389/fphys.2023.1272206. PMC 10830836. PMID 38304289.
  20. ^ a b "Uncharacterized membrane protein C3orf80". Protein. U.S. National Center for Biotechnology Information (NCBI). Retrieved 2024-09-21.
  21. ^ "PaxDb: Protein Abundance Database". pax-db.org. Retrieved 2024-12-05.
  22. ^ "C3orf80 - Antibodies - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2024-12-05.
  23. ^ "geneid:LOC401097". A comprehensive annotation of human, mouse and worm genes with mRNAs (ESTsAceView). U.S. National Center for Biotechnology Information (NCBI). Retrieved 2024-09-21.
  24. ^ "LOC103176350 uncharacterized membrane protein C3orf80 [Callorhinchus milii (elephant shark)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  25. ^ "C3orf80 C3orf80 homolog [Gallus gallus (chicken)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  26. ^ "C3orf80 orthologs". NCBI. Retrieved 2024-12-05.
  27. ^ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2024-12-05.
  28. ^ a b "EMBOSS Needle". www.ebi.ac.uk. Retrieved 2024-12-05.
  29. ^ "1110032F04Rik RIKEN cDNA 1110032F04 gene [Mus musculus (house mouse)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  30. ^ "C3H3orf80 chromosome 3 C3orf80 homolog [Antechinus flavipes (yellow-footed antechinus)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  31. ^ "C3H3orf80 chromosome 3 C3orf80 homolog [Sarcophilus harrisii (Tasmanian devil)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  32. ^ "C7H3orf80 chromosome 7 C3orf80 homolog [Alligator mississippiensis (American alligator)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  33. ^ "C9H3orf80 chromosome 9 C3orf80 homolog [Mauremys mutica (yellowpond turtle)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  34. ^ "C11H3orf80 chromosome 11 C3orf80 homolog [Prinia subflava (tawny-flanked prinia)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  35. ^ "C3orf80 C3orf80 homolog [Gallus gallus (chicken)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  36. ^ "C10H3orf80 chromosome 10 C3orf80 homolog [Aquila chrysaetos chrysaetos] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  37. ^ "C4H3orf80 chromosome 4 C3orf80 homolog [Pseudophryne corroboree (corroboree frog)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  38. ^ "C4H3orf80 chromosome 4 C3orf80 homolog [Bufo bufo (common toad)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  39. ^ "hypothetical protein NDU88_001183 [Pleurodeles waltl] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  40. ^ "C9H3orf80 chromosome 9 C3orf80 homolog [Rhinatrema bivittatum (two-lined caecilian)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  41. ^ "CCHR4.PART1H3orf80 chromosome chr4.part1 C3orf80 homolog [Protopterus annectens (West African lungfish)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  42. ^ "LOC102363136 uncharacterized membrane protein C3orf80 homolog [Latimeria chalumnae (coelacanth)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  43. ^ "LOC120531306 uncharacterized membrane protein C3orf80 homolog [Polypterus senegalus (gray bichir)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  44. ^ "LOC121609215 uncharacterized membrane protein C3orf80 homolog [Chelmon rostratus (copperband butterflyfish)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  45. ^ "c15h3orf80 chromosome 15 C3orf80 homolog [Danio rerio (zebrafish)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  46. ^ "LOC125457730 uncharacterized membrane protein C3orf80 homolog [Stegostoma tigrinum] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
  47. ^ "LOC103176350 uncharacterized membrane protein C3orf80 [Callorhinchus milii (elephant shark)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
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