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Chromosome 20 open reading frame 85

From Wikipedia, the free encyclopedia

Chromosome 20 open reading frame 85, or most commonly known as C20orf85 is a gene that encodes for the C20orf85 Protein (UniProt ID: Q9H1P6) . This gene is not yet well understood by the scientific community.

Background

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Aliases

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  • LLC1 - Low in Lung Cancer 1[1]
  • bA196N14.1[1]

Location

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It is found on chromosome 20, more specifically 20q13.32. It runs in the 5' to 3' direction on the top strand of chromosome 20. The gene HSPD1P19 or Heat Shock Protein Family D Member 1 Pseudogene 19 neighbors the gene, running before C20orf85, from the 5' to 3' end.[1]

RNA

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mRNA C20orf85 has 805 nucleotides which encodes for the C20orf85 protein.[2] So far this is the only known gene variant as of June 2022 and contains 4 exons. It has also been found to be expressed in samples of the testis, endometrium, and liver from HPA RNA-seq normal tissues.[1]

Protein

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This protein contains 137 Amino acids and is most commonly called "uncharacterized protein C20orf85",[3] or pfam14945. It has an approximate molecular weight of 15.5 kDa with an isoelectric point of 8.72.[2] C20orf85 protein is rich in the amino acids tryptophan and proline, compared to other human proteins.[4]

Structure

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According to iTasser and AlphaFold, the C20orf85 protein structure is predicted to have many more helices than sheets.

Protein Level Regulation

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The C20orf85 protein is predicted to be found in the extracellular space[5] or the cytoplasm, per PSORTII, DeepLoc 1.0, and DeepLoc 2.0. It is tissue specific, being expressed in the lungs, trachea, testis, and ovary.[1] There are also 3 predicted sites of SUMOylation and phosphorylation.

Evolution

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This graph shows that the human protein c20orf85 has a moderate evolution rate. This is compared to the orange trend-line of human cytochrome c which is known to evolve very slowly and the green trend-line of human fibrinogen alpha which is known to evolve at a very fast rate.

C20orf85 is predicted to evolve at a moderate pace, slower than the known fast evolving protein Fibrinogen Alpha but faster than the known slow evolving protein Cytochrome C.

Paralog

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Protein C20orf85 is paralogous with protein c2orf50. The two human proteins have been estimated to diverge from each other around 750 million years ago.

Orthologs

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This table is sorted by the most confident numerical value which is the date of divergence, then by the second most confident numerical value being sequence identity compared to the human c20orf85 protein. The colors are then sorted according to class.

C20orf85 has vast amounts of orthologs including mammals, reptiles, and birds. The table to the right shows a wide range of orthologs chosen because of the type of animal they were and the sequence identity.

Interacting Proteins

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C20orf85 has many interacting proteins, the proteins below were included because of their association to diseases and similarity in localization with C20orf85.

Abbreviated name Full name Basis of identification AND

What does it do?

Additional notes
MD2L2[6] Mitotic spindle assembly checkpoint protein MAD2B 2 hybrid prey

Adapter protein that interacts with various proteins

Nucleus and cytoplasm localization and is ubiquitously expressed

Fanconi anemia disease

FHL2[7] Four and a half LIM domains protein 2 Two hybrid prey Localized in the cytoplasm and nucleus

Many associated diseases

ALKBH7[8] Alpha-ketoglutarate-dependent dioxygenase alkB homolog 7, mitochondrial Validated 2 hybrid

A protein hydroxylase and isrequired to induce programmed necrosis

Mitochondrion matrix but expressed in the ovary, like c20orf85

No likely diseases

CNOT2[9] Trsncription complex subunit 2 2 Hybrid

Various cellular processes, esp in translation

Localization in the cytoplasm and nucleus

Involved in IDNADFS

CABP2[10] Calcium binding protein 2 2 Hybrid

Required for the inner hair cells of the ear

Localized in cytoplasm, cell membrane and golgi apparatus

Involved in autosomal recessive deafness

Clinical Significance

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Research conducted by Kyeong-Man Hong discovered that there is an inactivation of LLC1 (C20orf85) in some patients with non-small cell lung cancer but the reason for this is currently unknown.[11] The research titled "Immunohistochemical localization of LLC1 in human tissues and its limited expression in non-small cell lung cancer" found expression in the lung but no further findings have been evaluated from that article.[12]

Mutations

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There are many mutations found from the SNPs NCBI dataset of C20orf85,[13] these included below were mentioned as described in the "significance" column.

SNP Position

(aa)

Base Change Amino Acid Change Mutation Type Significance Clinical Significance
rs1207088890 7 A-->G Ser-->Gly Missense Highly conserved with phosphorylation site and O-beta-GlcNAc site None known
rs907822000 16 C-->T Leu-->Phe Missense Highly conserved None known
rs780117816 24 A-->T Lys--> N/A Nonsense Sumoylation site None known
rs200564315 100 G-->A Gly-->Ser Missense Highly conserved None known
rs754178666 137 A-->G His-->Arg Missense Important to localization None known

References

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  1. ^ a b c d e "C20orf85 chromosome 20 open reading frame 85 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-06-20.
  2. ^ a b "uncharacterized protein C20orf85 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-07-27.
  3. ^ "C20orf85 chromosome 20 open reading frame 85 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2022-06-20.
  4. ^ "Homo sapiens chromosome 20 open reading frame 85 (C20orf85), mRNA". 2021-04-16. {{cite journal}}: Cite journal requires |journal= (help)
  5. ^ "C20orf85 Gene - GeneCards | CT085 Protein | CT085 Antibody". www.genecards.org. Retrieved 2022-07-30.
  6. ^ "UniProt". www.uniprot.org. Retrieved 2022-07-30.
  7. ^ "UniProt". www.uniprot.org. Retrieved 2022-07-30.
  8. ^ "UniProt". www.uniprot.org. Retrieved 2022-07-30.
  9. ^ "UniProt". www.uniprot.org. Retrieved 2022-07-30.
  10. ^ "UniProt". www.uniprot.org. Retrieved 2022-07-30.
  11. ^ Hong, Kyeong-Man; Yang, Sei-Hoon; Chowdhuri, Sinchita R.; Player, Audrey; Hames, Megan; Fukuoka, Junya; Meerzaman, Daoud; Dracheva, Tatiana; Sun, Zhifu; Yang, Ping; Jen, Jin (2007-06-01). "Inactivation of LLC1 gene in nonsmall cell lung cancer". International Journal of Cancer. 120 (11): 2353–2358. doi:10.1002/ijc.22577. ISSN 0020-7136. PMC 1907378. PMID 17304513.
  12. ^ Chandra, V.; Choi, Y. B.; Hwang, H. L.; Lee, J. H.; Park, S. Y.; Kim, H. K.; Poojan, S.; Koh, J. S.; Kim, H. S.; Hong, K. M. (2015-08-10). "Immunohistochemical localization of LLC1 in human tissues and its limited expression in non-small cell lung cancer". Histology and Histopathology. 30 (30): 1111–1119. doi:10.14670/HH-11-608. ISSN 0213-3911. PMID 25786037.
  13. ^ "SNP linked to Gene (geneID:128602) Via Contig Annotation". www.ncbi.nlm.nih.gov. Retrieved 2022-07-30.