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Chromosome 20 open reading frame 111, or C20orf111, is the hypothetical protein that in humans is encoded by the C20orf111 gene.[1] C20orf111 is also known as Perit1 (peroxide inducible transcript 1), HSPC207, and dJ1183I21.1.[2] It was originally located using genomic sequencing of chromosome 20.[3] The National Center for Biotechnology Information, or NCBI,[1] shows that it is located at q13.11 on chromosome 20, however the genome browser at the University of California-Santa Cruz (UCSC) website[4] shows that it is at location q13.12, and within a million base pairs of the adenosine deaminase locus.[5] It was also found to have an increase in expression in cells undergoing hydrogen peroxide(H
2O
2)-induced apoptosis.[6] After analyzing the amino acid content of C20orf111, it was found to be rich in serine residues.
Gene
C20orf111 a valid, protein coding gene that is found on the minus strand of chromosome 20 at q13.12 by searching the UCSC Genome Browser,[4] but q13.11 according to Refseq on NCBI.[1]
Gene neighborhood
A few of the known genes near C20orf111 are given in the box below with their known function.
| Gene | Chromosomal Location | Strand | Function |
|---|---|---|---|
| Junctophilin 2 (JPH2) | 20q13.12 | Minus | Help facilitate the assembly of DHPR with other proteins of the excitation-contraction coupling machinery. Loss of function leads to cardiac-specific JPH2 deficiency and results in lower cardiac contractility[7] |
| TOX high mobility group box family member 2 (Tox2) | 20q13.12 | Plus | Shown to play a large role in transcription activation[8] |
| Adenosine deaminase (ADA) | 20q13.12 | Minus | Encodes an enzyme that catalyzes the hydrolysis of adenosine to inosine. Deficiency in this enzyme causes a form of severe combined immunodeficiency disease (SCID), in which there is dysfunction of both B and T lymphocytes with impaired cellular immunity and decreased production of immunoglobulins.[9] |
Transcript
General properties
- Genomic DNA Length:14,968 base pairs (bp)
- Most common mRNA Length: 2,260 bp with 4 exons. Has 10 splice isoforms.
- 5' untranslated region 252 bp long.
- 3' untranslated region 1,129 bp long.
Transcript variants
10 splice isoforms that encode good proteins, altogether 8 different isoforms, 2 of which are complete isoforms. The image below shows the 10 isoforms that are predicted.[11] Of these 10 splice isoforms, 8 have varying peptide lengths, however all of these proteins are only hypothetical with no extensive research done on them.[11]
Transcription regulation
When looking at the predicted promoter sequence,[12] there are no RNA Polymerase II binding sites, however there is a binding site for core promoter element for TATA-less promoters.[13] In this same region of the promoter, there is also a TATA-binding factor sequence, which helps in the positioning of RNA polymerase II for transcription.[14]
Protein
General properties
- Contains a highly conserved domain of unknown function 776 (DUF776),which composes 62% of the entire protein.
- Molecular weight 31.8 kilodaltons
- Isoelectric point 8.57
- Predicted to be a nuclear protein[16]
Function
The function of C20orf111 is not well understood by the scientific community. It does contain a domain of unknown function, DUF776, which has a large segment that is conserved well conserved through Xenopus tropicalus. It is also shown to have an increase in expression in rat cardiomyocytes undergoing hydrogen peroxide induced apoptosis.[6]
Expression
When looking at the EST Profiles in humans, normal tissue (non-cancerous), expresses at a level of 82 transcripts per million.[17] C20orf111 has been shown to increase in expression in rat cardiac myocytes undergoing |H|2|O|2|-induced apoptosis, suggesting a role in cell death.[6] In bladder, cervical, head and neck, non-neoplasia, pancreatic, and prostate cancer cells, there are expression levels lower than normal.
Homology
C20orf111 gene has no clear paralogs in the human genome. However, it has many orthologs in other organisms, and is conserved highly in organisms such as Xenopus tropicalis and is semi-conserved in the proto-animal Trichoplax adherens at the C-terminus.
The following table presents a select number of the orthologs found.[18]
| Scientific name | Common Name | Accession Number | Sequence Length(aa) | Percent Identity | Percent Similarity |
|---|---|---|---|---|---|
| Homo sapiens | Human | NP_057554.4 | 292 | - | - |
| Pan troglodytes | Chimpanzee | NP_001151026.1 | 292 | 99.7 | 99 |
| Ailuropoda melanoleuca | Giant Panda | XP_002917406 | 292 | 92 | 96 |
| Equus caballus | Horse | XP_001503005.1 | 292 | 91 | 96 |
| Mus musculus | Mouse | NP_079975 | 291 | 87 | 92 |
| Ornithorhynchus anatinus | Platypus | XP_001513001 | 293 | 66 | 73 |
| Gallus gallus | Chicken | NP_001025152 | 294 | 66 | 75 |
| Xenopus tropicalis | W.Clawed Frog | NP_988917 | 291 | 58 | 69 |
| Danio rerio | Zebrafish | XP_956651 | 300 | 45 | 59 |
| Nasonia vitripennis | Jewel Wasp | XP_003424720 | 271 | 58 | 14 |
| Drosophila melanogaster | Fruit Fly | NP_609391 | 287 | 47 | 18 |
| Trichoplax adhaerens | Trichoplax | XP_002114376 | 237 | 46 | 13 |
Conservation
The image below is a multiple sequence alignment comparing the conservation of the C20orf111 protein amongst other organisms. The protein is highly conserved in the DUF776 region amongst vertebrates, and also at the C-terminus in eukaryotes.
Predicted post-translational modification
Using tools at ExPASy[19] the following are predicted post-translational modifications for C20orf111.
- Predicted propeptide cleavage site in protein between position R81 and S82.[20]
- 30 predicted Serine phosphorylation sites
- 5 predicted Threonine phosphorylation sites
- 3 predicted Tyrosine phosphorylation sites[21]
Predicted secondary structure
PELE (Protein Secondary Structure Prediction) was used to predict the secondary structure of C20orf111. There is little in the way of β-strand or α-helix secondary structure, but a large part of the protein appears to exist as random coils. This is shown on the image of the C20orf111 images to the right.
References
- ↑ 1.0 1.1 1.2 EntrezGene 51526: C20orf111 chromosome 20 open reading frame 111
- ↑ Genecards
- ↑ Deloukas P, Matthews LH, Ashurst J, et al. (2001). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865–71. doi:10.1038/414865a. PMID 11780052.
- ↑ 4.0 4.1 UCSC Genome Search[permanent dead link]
- ↑ Shabtai F, Ben-Sasson E, Arieli S, Grinblat J (February 1993). "Chromosome 20 long arm deletion in an elderly malformed man". J. Med. Genet. 30 (2): 171–3. doi:10.1136/jmg.30.2.171. PMC 1016280. PMID 8445626.
- ↑ 6.0 6.1 6.2 Clerk A, Kemp TJ, Zoumpoulidou G, Sugden PH (April 2007). "Cardiac myocyte gene expression profiling during H2O2-induced apoptosis". Physiol. Genomics. 29 (2): 118–27. doi:10.1152/physiolgenomics.00168.2006. PMID 17148688.
- ↑ Golini L, Chouabe C, Berthier C, Cusimano V, Fornaro M, Bonvallet R, Formoso L, Giacomello E, Jacquemond V, Sorrentino V (December 2011). "Junctophilin 1 and 2 proteins interact with the L-type Ca2+ channel dihydropyridine receptors (DHPRs) in skeletal muscle". J. Biol. Chem. 286 (51): 43717–25. doi:10.1074/jbc.M111.292755. PMC 3243543. PMID 22020936.
- ↑ Tessema M, Yingling CM, Grimes MJ, Thomas CL, Liu Y, Leng S, Joste N, Belinsky SA (2012). "Differential Epigenetic Regulation of TOX Subfamily High Mobility Group Box Genes in Lung and Breast Cancers". PLoS ONE. 7 (4): e34850. doi:10.1371/journal.pone.0034850. PMC 3319602. PMID 22496870.
- ↑ Valerio D, Duyvesteyn MG, Dekker BM, Weeda G, Berkvens TM, van der Voorn L, van Ormondt H, van der Eb AJ (February 1985). "Adenosine deaminase: characterization and expression of a gene with a remarkable promoter". EMBO J. 4 (2): 437–43. PMC 554205. PMID 3839456.
- ↑ NCBI (National Center for Biotechnology Information)
- ↑ 11.0 11.1 AceView
- ↑ Genomatix ElDorado
- ↑ Tokusumi Y, Ma Y, Song X, Jacobson RH, Takada S (March 2007). "The new core promoter element XCPE1 (X Core Promoter Element 1) directs activator-, mediator-, and TATA-binding protein-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters". Mol. Cell. Biol. 27 (5): 1844–58. doi:10.1128/MCB.01363-06. PMC 1820453. PMID 17210644.
- ↑ Wikipedia:TATA-binding Protein
- ↑ SDSC Biology Workbench 2.0
- ↑ "PSORTII Prediction".
- ↑ 17.0 17.1 "EST Profile - Hs.75798". UniGene. National Center for Biotechnology Information.
- ↑ NCBI BLAST: Basic Local Alignment Search Tool
- ↑ ExPASy Proteomics Server
- ↑ Chang WC, Lee TY, Shien DM, Hsu JB, Horng JT, Hsu PC, Wang TY, Huang HD, Pan RL (November 2009). "Incorporating support vector machine for identifying protein tyrosine sulfation sites". J Comput Chem. 30 (15): 2526–37. doi:10.1002/jcc.21258. PMID 19373826.
- ↑ Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites". J. Mol. Biol. 294 (5): 1351–62. doi:10.1006/jmbi.1999.3310. PMID 10600390.
External links
- Human OSER1 genome location and OSER1 gene details page in the UCSC Genome Browser.