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Chromosome 20 open reading frame 111, or C20orf111, is the hypothetical protein encoded by the C20orf111 gene. [1] C20orf111 has many common names, including Perit1 (Peroxide inducible transcript 1), HSPC207, dJ1183I21.1, OTTHUMP00000031041, oxidative stress responsive 1. [2] It was originally located using genomic sequencing of chromosome 20. [3] NCBI [4] shows that it is at location q13.11 on chromosome 20, however BLAT [5]shows that it is at location q13.12, and within a million base pairs of the adenosine deaminase locus. [6]
Gene
[edit]C20orf111 a valid, protein coding gene that is found on the minus strand of chromosome 20 at q13.12 according to BLAT, [5], but q13.11 according to NCBI. [4]
![The location of the C20orf111 gene on chromosome 20 according to BLAT, [5]](http://en.wikipedia.org/wiki/Special:Upload?wpDestFile=Perti1_Chromosomal_Location_according_to_BLAT..png){kind=link}
Gene Neighborhood
[edit]C20orf111 has many genes in it's neighborhood upstream and downstream on the minus and also the plus strand of the chromosome. 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
[edit]- Genomic DNA Length:14,968 base pairs (bp)
- mRNA Length: 2,260 bp with 4 exons.
- 5' untranslated region 252 bp long.
- 3' untranslated region 1,129 bp long.
Transcript Variants
[edit]
According to AceView, [10] 10 splice isoforms that encode good proteins, altogether 8 different isoforms, 2 of which are complete isoforms. The image below is also from AceView and shows the 10 isoforms that are predicted[10].
Transcription Regulation
[edit]When looking at the predicted promoter sequence given by Genomatix[11], there are no RNA Polymerase II binding sites, however there is a binding site for core promoter element for TATA-less promoters.[12] 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.[13]
Protein
[edit]- Contains a highly conserved domain of unknown function 776 (DUF776)
- Molecular weight 31.8 kilodaltons
- Isoelectric point 8.57
- Predicted to be a nuclear protein[15]
Function
[edit]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 in most mammals and the amphibians such as the western clawed frog. It is also shown to have an increase in expression in rat cardiomyocytes undergoing hydrogen peroxide induced apoptosis.[16]
Expression
[edit]When looking at the EST Profiles in humans given by NCBI, normal tissue (non-cancerous), expresses at a level of 82 transcripts per million. [17] In one published article in Physiological Genomics, they showed that Perit1 expression is increased in cardiac myocytes undergoing H2O2-induced apoptosis, suggested a role in cell death.[18] In many cancer cells, there are expression levels higher than normal, like in breast cancer cells, and in leukemia. However, in prostate cancer, pancreatic cancer, and lung cancer cells the levels of expression of Perit1 is lower than normal tissue.[17]
Homology
[edit]C20orf111 gene has no true 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 C-terminus in Trichoplax adherens.
The following table presents some of the orthologs found using searches in BLAST[20]and BLAT. [5] This list isn’t complete, but shows the conservation of the Perit1 protein throughout evolutionary history.
| 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 |
Predicted Post-Translational Modification
[edit]
Using various tools at ExPASy[21] the following are possible post-translational modifications for Perit1.
- Predicted propeptide cleavage site in protein between position R81 and S82.[22]
- Predicted Sulfation Site at Y237 [23]
- 30 predicted Serine phosphorylation sites
- 5 predicted Threonine phosphorylation sites
- 3 predicted Tyrosine phosphorylation sites [24]
Predicted Secondary Structure
[edit]PELE (Protein Secondary Structure Prediction) was used to predict the secondary structure of C20orf111. There are no regions that are rich in either β-sheet and α-helix, but there are many random coils formed. This is shown on the image of the C20orf111 images above.
References
[edit]- ^ Entrez
- ^ Genecards
- ^ [Deloukas, P; Matthews, L.H.; Ashurst, J; et al. (2001). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414: 865–871.
{{cite journal}}: Explicit use of et al. in:|last4=(help)] - ^ a b c NCBI (National Center of Biotechnology Information) Cite error: The named reference "NCBI" was defined multiple times with different content (see the help page).
- ^ a b c d BLAT Search Genome
- ^ [Shabtai, I; et al. (1993). "Chromosome 20 long arm deletion in an elderly malformed man". Medical Genetics. 30: 171–173.
{{cite journal}}: Explicit use of et al. in:|last2=(help)] - ^ [Golini, L; Chouabe, C; Berthier, C; Cusimano, V (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.
- ^ [Tessema, M; Yingling, C; Grimes, M; Thomas, C (2012). "Differential Epigenetic Regulation of TOX Subfamily High Mobility Group Box Genes in Lung and Breast Cancers". PLoS One. 7 (4).
- ^ [Valerio, D; Duyvesteyn, M; Dekker, B; Weeda, G (1985). "Adenosine deaminase: characterization and expression of a gene with a remarkable promoter". EMBO J. 4 (2).
- ^ a b AceView
- ^ Genomatix ElDorado
- ^ [Tokusumi, Y; Ma, Ylast3=Song; Jacobson, H (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.
{{cite journal}}:|first3=missing|last3=(help); Text "Pages: 1844-1858" ignored (help); line feed character in|title=at position 4 (help)CS1 maint: numeric names: authors list (link) - ^ Wikipedia:TATA-binding Protein
- ^ SDSC Biology Workbench 2.0
- ^ "PSORTII Prediction".
- ^ [Clerk, A; Kemp, TJ; Zoumpoulidou, G; Sugden, PH (2006). "Cardiac myocyte gene expression profiling during H2O2-induced apoptosis". Physiol Genomics. 29 (2): 118–27.
- ^ a b EST Profile Viewer- Human
- ^ [Clerk, A; Kemp, TJ; Zoumpoulidou, G; Sugden, PH (2006). "Cardiac myocyte gene expression profiling during H2O2-induced apoptosis". Physiol Genomics. 29 (2): 118–27.
- ^ [1]
- ^ NCBI BLAST: Basic Local Alignment Search Tool
- ^ ExPASy Proteomics Server
- ^ [Duckert, P; Brunak, S; Blom, N (2004). "Prediction of proprotein convertase cleavage sites". Protein Engineering. 17: 107–112.]
- ^ [Chang, W; Lee, T; et al. (2004). "Incorporating support vector machine for identifying protein tyrosine sulfation sites". Journal of computational chemistry.
{{cite journal}}: Explicit use of et al. in:|last3=(help)] - ^ [Blom, N; Gammeltoft, S; Brunak, S (1999). "Sequence and structure based prediction of eukaryotic protein phosphorylation sites". Journal of Molecular Biology. 294: 1351–1362.]