User:Lin8064/sandbox
C17orf64 is a protein, which in humans is encoded by the C17orf64 gene. Evidence from protein interaction experiments show that this protein interacts with other proteins that are responsible for processes, such as DNA replication, transcription, and regulation of expression[1]. Subcellular localization experiments show that expression of the protein has been found in the nucleus and vesicles, suggesting that the function involves endocytosis [2]. These observations together do not agree with each other, but more research into this protein could lead to more clarification about the function.
Gene
[edit]This gene is located on the plus strand at 17q23.2 and spans from 58,499,953 to 58,508,627 bp [3]. USP32 or Ubiquitin Specific Peptidase 32 flanks C17orf64 on the minus strand [3].
mRNA Transcripts
[edit]The C17orf64 gene produces five other isoforms. These isoforms differ due to the start of transcription, where the promoter sequence is located [3]. This table illustrates the differences among the various forms of the gene.
| Name | Reference Sequence Number | Number of base-pairs | Number of amino acid residues |
|---|---|---|---|
| C17orf64 | NM_181707.2 | 977 | 236 |
| C17orf64 transcript variant X1 | XM_005257033.4 | 1,030 | 279 |
| C17orf64 transcript variant X2 | XM_005257034.4 | 1,256 | 269 |
| C17orf64 transcript variant X3 | XM_005257035.4 | 934 | 209 |
| C17orf64 transcript X4 | XM_017024166.1 | 946 | 199 |
| C17orf64 transcript X5 | XM_005257036.2 | 999 | 246 |
Protein Structure
[edit]
C17orf64 contains:[4]
- One DUF4208 region
- Number of Residues-236 amino acids
- Molecular weight-27.1 kilodaltons
- Isoelectric point-9.4
The secondary structure of C17orf64 is predicted to consist of alternating pairs of alpha helices and random coils[4].
Expression
[edit]Based on human tissue EST profiles, C17orf64 appears to be normally expressed at high levels in the testes. Low levels of expression are found in areas, such as the brain, liver, and lungs [5]. C17orf64 expression levels appears to be higher in CD4+ cells in individuals with Multiple Sclerosis compared to the control group. This suggests that C17orf64 expression is related to the immune system [6].
Function
[edit]The function of C17orf64 has not yet been established in scientific literature. The evidence from immunohistochemistry experiments verify that this protein is found in the nucleus and vesicles, suggesting that this protein is involved in endocytosis [2].
Protein Interactions
[edit]A diverse collection of proteins that interact with C17orf64 are put into this table along with their function, experimental verification, and likelihood of interaction [1].
| Name | Function | Verification Experiments | Probability |
|---|---|---|---|
| UBA1 | Catalyzes the first step in ubiquitin conjugation to mark cellular proteins for degradation through the ubiquitin- proteasome system | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.806 |
| PRIM1 | DNA primase serves a polymerase that synthesizes small RNA primers for the Okazaki fragments | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.815 |
| POLR2B | RNA Polymerase II | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.596 |
| POLR3B | RNA Polymerase III | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.595 |
| TAF1L | TATA binding protein | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.700 |
| ASH1L | Histone methyltransferases that methylated ‘Lys-36’ of histone 3 (in Drosophila) | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.683 |
| TAF1 | TATA binding protein-associated factor, TAF1 RNA Polymerase II | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.632 |
| INO80 | DNA helicase (S. cerevisiae) | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.605 |
| SETD1A | Histone methyltransferases that specifically methylated ‘Lys-4’ of histone 3 when it is part of HMT complex, not if ‘Lys-9’ residue already methylated | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.598 |
| SETD1B | Histone methyltransferases that specifically methylated ‘Lys-4’ of histone 3 when it is part of HMT complex, not if ‘Lys-9’ residue already methylated | *Protein-protein interactions (two hybrid pooling assay) in Plasmodium falciparum | 0.598 |
Predicted Post-Translational Modifications and Motifs
[edit]
Using various tools at ExPASy[7] the following are possible post-translational modifications and protein motifs for C17orf64.
- 3 O-Beta GLNAc sites
- 1 Caspase 3-7 site
- 2 MAPK Phosphorylation Sites
- 1 PKA Phosphorylation Site
- 1 Cyclin Site
- 1 CKI Phosphorylation Site
- 1 Sumoylation Site
- Monoclonal Nuclear Localization Site
These post-translational modification and motif sites are conserved in vertebrates.
Homology
[edit]C17orf64 has two paralogs-CHD1 and CHD2. It does have orthologs within eukaryotes. The following table presents some of the orthologs found using searches in BLAST[8]and BLAT [9]. This list does not contain all of the orthologs for C17orf64. It is meant to display the diversity of species for which orthologs are found.
| Scientific name | Common Name | Accession Number | Sequence Length | Percent Identity | Percent Similarity |
|---|---|---|---|---|---|
| Homo Sapiens | Human | NP_859058.2 | 236 | - | - |
| Macaca fascicularis | Crab-eating Macaque | XP_005583956.1 | 236 | 91 | 96 |
| Ovis aries | Sheep | XP_004012475.1 | 232 | 73 | 86 |
| Psgoscelis adeliae | Adelie Penguin | XP_009322600.1 | 321 | 52 | 65 |
| Gavialis gangeticus | Fish-eating crocodile | XP_019366853.1 | 262 | 51 | 60 |
| Anolis carolinensis | Green anole | XP_008117671.1 | 304 | 50 | 59 |
| Columbia livia | Rock Dove | XP_005503326.1 | 218 | 49 | 64 |
| Apis cerana cerana | Eastern honey bee | PBC34575.1 | 1814 | 42 | 46 |
| Nilaparvata lugens | Brown planthopper | XP_022197424.1 | 1494 | 42 | 41 |
| Xenopus laevis | African Clawed Frog | OCT89769.1 | 1827 | 38 | 5.4 |
| Salmo salar | Atlantic Salmon | XP_014000422.1 | 1800 | 37 | 52 |
| Oncorhynchus mykiss | Rainbow Trout | XP_021457277.1 | 1800 | 37 | 52 |
| Xenopus tropicalis | Western Clawed Frog | OCA51862.1 | 1694 | 36 | 7 |
| Daphnia magna | Water flea | KZS05523.1 | 540 | 34 | 17 |
| Limulus polyphemus | Atlantic horseshoe crab | XP_022239171.1 | 1823 | 34 | 46 |
| Phellinus noxius | Brown tea root disease | PAV18799.1 | 1455 | 34 | 40 |
| Lodderomyces elongisporus | Yeast | EDK43371.1 | 1500 | 31 | 46 |
References
[edit]- ^ a b Protein Interactions (C17orf64)
- ^ a b Subcellular Experiments
- ^ a b c NCBI gene C17orf64
- ^ a b SDSC Biology Workbench 2.0
- ^ EST Profile Viewer- Human
- ^ Somma P, Ristori G, Battistini L, Cannoni S, Borsellino G, Diamantini A, Salvetti M, Sorrentino R, Fiorillo MT (November 2006). "Characterization of CD8+ T cell repertoire in identical twins discordant and concordant for multiple sclerosis". Journal of Leukocyte Biology. 81 (3): 696–710.
- ^ ExPASy Proteomics Server
- ^ NCBI BLAST: Basic Local Alignment Search Tool
- ^ BLAT Search Genome