TMEM63A | |||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Identifiers | |||||||||||||||||||||||||||||||||||||||||||||||||||
Aliases | TMEM63A , KIAA0792, transmembrane protein 63A, HLD19 | ||||||||||||||||||||||||||||||||||||||||||||||||||
External IDs | MGI: 2384789 HomoloGene: 101673 GeneCards: TMEM63A | ||||||||||||||||||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||||||||||||||||||
| |||||||||||||||||||||||||||||||||||||||||||||||||||
Wikidata | |||||||||||||||||||||||||||||||||||||||||||||||||||
|
Transmembrane protein 63A is a protein that in humans is encoded by the TMEM63A gene. [5] [6] [7] The mature human protein is approximately 92.1 kilodaltons (kDa), with a relatively high conservation of mass in orthologs. [8] The protein contains eleven transmembrane domains and is inserted into the membrane of the lysosome. [9] [10] BioGPS analysis for TMEM63A in humans shows that the gene is ubiquitously expressed, with the highest levels of expression found in T-cells and dendritic cells. [11]
TMEM63A is located on the negative DNA strand of chromosome 1 at location 1q42.12, spanning base pairs 226,033,237 to 226,070,069. [7] Aliases include KIAA0489 and KIAA0792. The human gene product is a 4,469 base pair mRNA with 25 predicted exons. [12] There are 9 predicted splice isoforms of the gene, three of which are protein coding. Promoter analysis was carried out using El Dorado [13] through the Genomatix software page. The predicted promoter region spans 971 base pairs, from 226,070,920 to 226,069,950 on the negative strand of chromosome 1.
TMEM63A is located adjacent to the EPHX1 gene on the positive sense strand of DNA on chromosome 1, as well as the LEFTY1 gene on the negative sense strand. [7] Other genes in the same area on chromosome 1 include SRP9 and LEFTY3 on the positive strand, and MIR6741 and PYCR2 on the negative strand.
TMEM63 is ubiquitously expressed throughout the human body at varying levels, occurring with the highest relative prevalence in CD 8+ T cells and CD 4+ T cells. [11] [14] Moderate relative levels of expression are also observed throughout the brain, particularly in the occipital lobe, parietal lobe, and pancreas. [14] Analysis of TMEM63A expression in the mouse using BioGPS revealed more variable expression patterns, with the highest expression being seen in the stomach and large intestine. [11] Using the El Dorado program from Genomatix, transcription factor regulation was predicted, which found that ‘’TMEM63A’’ is highly regulated by E2F cell cycle regulators and EGR1, a factor believed to be a tumor suppressor gene with expression in the brain. [13] The 3’ UTR is predicted to be bound by the regulatory element miR-9/9ab. [15]
The mature form of the human TMEM63A protein has 807 amino acid residues with an isoelectric point of 6.925. [8] This is fairly conserved across orthologs. A BLAST alignment revealed that the protein contains three domains: RSN1_TM and two domains of unknown function (DUF4463 and DUF221). [16] RSN1_TM is predicted to be involved in Golgi vesicle transport and exocytosis. DUF4463 is cytosolic and distantly homologous to RNA-binding proteins. This domain can be used to determine the orientation of the protein in the membrane, with the N-terminus of the protein being within the lysosome and the C-terminus located in the cytosol.
Post-translational modification has been determined both experimentally and using bioinformatic analysis. There are two likely sites of glycosylation on the protein: N38 and N450. [17] These were predicted using the NetNGlyc program from ExPASy and the TMEM63A amino acid sequence, as well as the inferred orientation of the protein in the membrane. [18] There are three likely sites of phosphorylation on the protein: S85, S98, and S735, which were predicted using the NetPhos program. [19]
The protein has three isoforms. The mature protein is designated isoform CRA. The other two isoforms are X1 and X2, which are 630 amino acid residues and 468 amino acid residues long, respectively. Isoform X1 is missing the N-terminus of the mature protein, while isoform 2 is missing the C-terminus. [8]
Using text-based information, TMEM63A is thought to potentially interact with six other proteins: EEF1D, [20] FAM163B, CPNE9, TMEM90A, STAC2, HEATR3, and WDR67. [21]
The function of TMEM63A is not known, although one study found it was in a region likely regulated by mir-200a, linked to epithelial homeostasis. [22] Another found it to be in a quantitative trait locus linked to haloperidol-induced catalepsy. [23]
TMEM63A has two paralogs: TMEM63B, which is located at 6p21.1, and TMEM63C, which is located at C14orf171. [24] Alignment between them shows that TMEM63C is more closely related to TMEM63B than TMEM63A. [8] A BLAST alignment showed homology of TMEM63A and TMEM63B to proteins as distantly related as plants, while TMEM63C was homologous only as distantly as in drosophila. [16] This indicates that TMEM63C likely diverged from the two early in invertebrates.
TMEM63A has a large ortholog space, with homologs present in organisms as distantly related as plants.
Genus and species | Common name | Class | Accession | Percent identity |
---|---|---|---|---|
Otolemur garnettii | Bush baby | Mammalia | XP_003791028.1 | 91% |
Vicugna pacos | Alpaca | Mammalia | XP_006198896.1 | 92% |
Mus musculus | Mouse | Mammalia | NP_659043.1 | 90% |
Trichechus manatus latirostris | West Indian manatee | Mammalia | XP_004375949.1 | 89% |
Canis lupus familiaris | Dog | Mammalia | NP_001274088.1 | 89% |
Myotis davidii | Mouse-eared bat | Mammalia | XP_006761379.1 | 80% |
Pelodiscus sinensis | Chinese softshell turtle | Sauropsida | XP_006118107.1 | 71% |
Alligator sinensis | Chinese alligator | Reptilia | XP_006016630.1 | 70% |
Ficedula albicollis | Collared flycatcher | Aves | XP_005043078.1 | 69% |
Gallus gallus | Red junglefowl | Aves | XP_419384.3 | 68% |
Xenopus tropicalis | Western clawed frog | Amphibia | NP_001072343.1 | 65% |
Ictalurus punctatus | Channel catfish | Actinopterygii | AHH42519.1 | 54% |
Culex quinquefasciatus | Southern house mosquito | Insecta | XP_001861445.1 | 34% |
Clonorchis sinensis | Chinese liver fluke | Trematoda | GAA53916.1 | 23% |
Oryza sativa | Asian rice | Liliopsida | NP_001065504.1 | 20% |
Protein YIF1A is a Yip1 domain family proteins that in humans is encoded by the YIF1A gene.
E3 ubiquitin-protein ligase RNF128 is an enzyme that in humans is encoded by the RNF128 gene.
HIKESHI is a protein important in lung and multicellular organismal development that, in humans, is encoded by the HIKESHI gene. HIKESHI is found on chromosome 11 in humans and chromosome 7 in mice. Similar sequences (orthologs) are found in most animal and fungal species. The mouse homolog, lethal gene on chromosome 7 Rinchik 6 protein is encoded by the l7Rn6 gene.
Tetratricopeptide repeat 39A is a human protein encoded by the TTC39A gene. TTC39A is also known as DEME-6, KIAA0452, and c1orf34. The function of TTC39A is currently not well understood. The main feature within tetratricopeptide repeat 39A is the domain of unknown function 3808 (DUF3808), spanning almost the entire protein. KIAA0452 can also be seen as an isoform of TTC39A because of differences in genome sequence, but overlap in DUF domain.
Protein FAM214A, also known as protein family with sequence similarity 214, A (FAM214A) is a protein that, in humans, is encoded by the FAM214A gene. FAM214A is a gene with unknown function found at the q21.2-q21.3 locus on Chromosome 15 (human). The protein product of this gene has two conserved domains, one of unknown function (DUF4210) and another one called Chromosome_Seg. Although the function of the FAM214A protein is uncharacterized, both DUF4210 and Chromosome_Seg have been predicted to play a role in chromosome segregation during meiosis.
TMEM249 is a protein that in humans is encoded by the C8orfk29 gene.
TMEM44 is a protein that in humans is encoded by the TMEM44 gene. DKFZp686O18124 is a synonym of TMEM44.
Chromosome 9 open reading frame 43 is a protein that in humans is encoded by the C9orf43 gene. The gene is also known as MGC17358 and LOC257169. C9orf43 contains DUF 4647 and a polyglutamine repeat region although protein function is not well understood.
Chromosome 9 open reading frame 50 is a protein that in humans is encoded by the C9orf50 gene. C9orf50 has one other known alias, FLJ35803. In humans the gene coding sequence is 10,051 base pairs long, transcribing an mRNA of 1,624 bases that encodes a 431 amino acid protein.
LOC101928193 is a protein which in humans is encoded by the LOC101928193 gene. There are no known aliases for this gene or protein. Similar copies of this gene, called orthologs, are known to exist in several different species across mammals, amphibians, fish, mollusks, cnidarians, fungi, and bacteria. The human LOC101928193 gene is located on the long (q) arm of chromosome 9 with a cytogenic location at 9q34.2. The molecular location of the gene is from base pair 133,189,767 to base pair 133,192,979 on chromosome 9 for an mRNA length of 3213 nucleotides. The gene and protein are not yet well understood by the scientific community, but there is data on its genetic makeup and expression. The LOC101928193 protein is targeted for the cytoplasm and has the highest level of expression in the thyroid, ovary, skin, and testes in humans.
Leucine rich single-pass membrane protein 2 is a single-pass membrane protein rich in leucine, that in humans is encoded by the LSMEM2 gene. The LSMEM2 protein is conserved in mammals, birds, and reptiles. In humans, LSMEM2 is found to be highly expressed in the heart, skeletal muscle and tongue.
Family with Sequence Similarity 155 Member B is a protein in humans that is encoded by the FAM155B gene. It belongs to a family of proteins whose function is not yet well understood by the scientific community. It is a transmembrane protein that is highly expressed in the heart, thyroid, and brain.
TMEM275 is a protein that in humans is encoded by the TMEM275 gene. TMEM275 has two, highly-conserved, helical trans-membrane regions. It is predicted to reside within the plasma membrane or the endoplasmic reticulum's membrane.
Transmembrane protein 169 (TMEM169) in humans is encoded by TMEM169 gene. The aliases of TMEM169 include FLJ34263, DKFZp781L2456, and LOC92691. TMEM169 has the highest expression in the brain, particularly the fetal brain. TMEM169 has homologs mammals, reptiles, amphibians, birds, fish, chordates and invertebrates. The most distantly related homolog of TMEM169 is Anopheles albimanus.
Chromosome 9 open reading frame 85, commonly known as C9orf85, is a protein in Homo sapiens encoded by the C9orf85 gene. The gene is located at 9q21.13. When spliced, four different isoforms are formed. C9orf85 has a predicted molecular weight of 20.17 kdal. Isoelectric point was found to be 9.54. The function of the gene has not yet been confirmed, however it has been found to show high levels of expression in cells of high differentiation.
Transmembrane protein 101 (TMEM101) is a protein that in humans is encoded by the TMEM101 gene. The TMEM101 protein has been demonstrated to activate the NF-κB signaling pathway. High levels of expression of TMEM101 have been linked to breast cancer.
Coiled-Coil Domain Containing 190, also known as C1orf110, the Chromosome 1 Open Reading Frame 110, MGC48998 and CCDC190, is found to be a protein coding gene widely expressed in vertebrates. RNA-seq gene expression profile shows that this gene selectively expressed in different organs of human body like lung brain and heart. The expression product of c1orf110 is often called Coiled-coil domain-containing protein 190 with a size of 302 aa. It may get the name because a coiled-coil domain is found from position 14 to 72. At least 6 spliced variants of its mRNA and 3 isoforms of this protein can be identified, which is caused by alternative splicing in human.
Transmembrane protein 212 is a protein that in humans is encoded by the TMEM212 gene. The protein consists of 5 transmembrane domains and localizes in the plasma membrane and endoplasmic reticulum. TMEM212 has orthologs in vertebrates but not invertebrates. TMEM212 has been associated with sporadic Parkinson's disease, facial processing, and adiposity in African Americans.
Transmembrane Protein 269 (TMEM269) is a protein which in humans is encoded by the TMEM269 gene.
C10orf53 is a protein that in humans is encoded by the C10orf53 gene. The gene is located on the positive strand of the DNA and is 30,611 nucleotides in length. The protein is 157 amino acids and the gene has 3 exons. C10orf53 orthologs are found in mammals, birds, reptiles, amphibians, fish, and invertebrates. It is primarily expressed in the testes and at very low levels in the cerebellum, liver, placenta, and trachea.
{{cite journal}}
: Cite journal requires |journal=
(help)