| YIF1A | |||||||||||||||||||||||||||||||||||||||||||||||||||
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| Identifiers | |||||||||||||||||||||||||||||||||||||||||||||||||||
| Aliases | YIF1A , 54TM, FinGER7, YIF1, YIF1P, Yip1 interacting factor homolog A, membrane trafficking protein | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | OMIM: 611484; MGI: 1915340; HomoloGene: 56295; GeneCards: YIF1A; OMA:YIF1A - orthologs | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Protein YIF1A is a Yip1 domain family proteins that in humans is encoded by the YIF1A gene. [5] [6] [7] [8]
YIF1A (Yip1 interacting factor homolog A) is also known as YIF1, YIF1P, FinGER7, and 54TM. [9] It has 4,591 base pairs with 8 exons, and it is located on the minus strand of chromosome 11, at 11q13.2, in humans. [10]
There are four predicted promoter for YIIF1A. [11] The predicted promoter region with highest confidence is GXP_50494 and has 1252 base pairs long; it extends past the first exon of YIF1A. This promoter is located on the minus strand of chromosome 11.
The promoter of YIF1A transcript variant 1 contains numerous transcription factor binding sites. [12] Transcription factors predicted to bind to the promoter region include the following.
The expression of YIF1A is highest in the duodenum and liver. It is also expressed at moderate levels in tissues including the colon, ovary, pancreases, spleen, and esophagus, and expressed at lower levels in a variety of other tissues. [13] [14] [15] NCBI GeoProfile data provide the tissue expression graph for YIF1A in humans; it also indicates that YIF1A is expressed at moderately to moderately low across all other tissues. [16]
YIF1A has isoforms 1 and 2, with exons 8 and 7 respectively. [10] The two transcripts undergo alternate splicing and are translated into proteins with 293 and 241 amino acids, respectively. [17] [18]
The 5' untranslated region has predicted sites for binding by RBXM, EIF4B, and FUS. The 3' untranslated region has predicted sites for binding by ELAVL1, which is AU rich elements and regulate mRNA stability. [19]
The longest protein isoform of YIF1A is 293 amino acids in length. It has an observed molecular weight of approximately 32.0 kDa with a predicted isoelectric point of approximately 8.98. [18] [20] [21]
YIF1 is a very normal protein in terms of the amino acid quantities it contains. The composition of each amino acid residue is similar to its average relative composition among human proteins. There are no charge clusters, runs, or patterns. There is a repetitive structure for protein YIF1A at [ 201- 204 and 288- 291 ] TFHL. [20]
YIF1A has a conserved domain, pfam03878 (AA 57 →287). [10] Within the domain, there are 5 transmembrane domains, 3 non-cytosolic domains, and 3 cytosolic domains. It has been hypothesized that there is a possible role in transport between the endoplasmic reticulum and Golgi. [9]
The structure of YIF1A consist of approximately 59% alpha-helices, with TM helix and disordered regions making up the rest of the structure; no beta- strand was predicted. [24]
YIF1A's predicted location is in the endoplasmic reticulum, with intracellular N-terminus and an extracellular C-terminus. [25] [26]
YIF1A undergoes methionine cleavage and N-terminal acetylation, which is one of the most common post translation modifications of eukaryotic proteins. [27] It also phosphorylated by unspecified kinases at several sites. [28] Three glycation site is predicted in lysine residue(lys 104,161, and 211). [29] YIF1A undergoes O-ß-GlcNAc modification at 5 sites, 1 of them being Yin-Yang sites. [30]
Based on fluorescence microscopy, validated two hybrid, and anti tag coimmunoprecipitation, the protein that is most likely to interact with YIF1A are GPR37, SEC23IP, REEP2, and YIPF5. Studies suggest that interaction between VAPB and YIF1A control membrane delivery into dendrites. [31] It also participates in ER unfolded protein response (UPR) by inducing ERN1/IRE1. [32] Additionally, the YIF1A protein interacts with the M protein of SARS-Cov-2. [33]
YIF1A has a single Paralog called YIF1B, which is located on human chromosome 19. [9] YIF1A has 238 identified orthologs. [34] The ortholog contains vertebrates such as mammals, amphibians, and reptiles. It also has invertebrates species such as Insecta, Anthozoa, and Ascidiacea. No ortholog was found in protists, bacteria, or archaea.
The following table provides a sample of the ortholog of YIF1A.
| Genus and species | Accession Number [10] | Date of Divergence (MYA) [35] | Sequence Length(AA) | Sequence Identity [36] |
|---|---|---|---|---|
| Homo sapiens (Human) | NP_065203 | 0 | 293 | 100 |
| Aotus nancymaae (Ma's night monkey) | XP_012318344 | 43 | 317 | 94 |
| Mus musculus (Mouse) | NP_080829 | 90 | 293 | 93 |
| Sus scrofa (Wild Boar) | XP_013849519 | 96 | 311 | 92 |
| Delphinapterus leucas (White whale) | XP_022447094 | 96 | 306 | 91 |
| Phascolarctos cinereus (Koala) | XP_020823757 | 159 | 293 | 88 |
| Ornithorhynchus anatinus (Platypus) | XP_028915982 | 177 | 293 | 88 |
| Chelonia mydas (Green turtle) | XP_007056281 | 312 | 240 | 78 |
| Chrysemys picta bellii (Painted turtle) | XP_005305497 | 312 | 293 | 73 |
| Microcaecilia unicolor (Amph.) | XP_029470520 | 352 | 306 | 72 |
| Rhinatrema bivittatum (Two-lined caecilian) | XP_029470520 | 352 | 307 | 71 |
| Latimeria chalumnae (Gombessa) | XP_014345204 | 413 | 296 | 71 |
| Salmo trutta (Brown trou) | XP_029585843 | 435 | 309 | 70 |
| Echeneis naucrates (live sharksucker) | XP_029368074 | 435 | 308 | 66 |
| Danio rerio (Zebrafish) | NP_956225 | 435 | 307 | 65 |
| Maylandia zebra (zebra mbuna) | XP_004545672 | 435 | 308 | 63 |
| Saccharomyces cerevisiae S288C (Baker's yeast) | NP_014136 | 1017 | 314 | 33 |
| Physcomitrium patens (moss) | XP_024362517 | 1275 | 282 | 30 |
C11orf49 is a protein coding gene that in humans encodes for the C11orf49 protein. It is heavily expressed in brain tissue and peripheral blood mononuclear cells, with the latter being an important component of the immune system. It is predicted that the C11orf49 protein acts as a kinase, and has been shown to interact with HTT and APOE2.
The FAM185A is a protein that in humans is encoded by the FAM185A gene. The FAM185A gene is found on the positive strand of Chromosome 7 at 7q22.1. The gene begins 102,389,399bp from the p-terminus of the chromosome and ends at 102,449,672bp from the p-terminus; it covers a total of 73,308 basepairs. The protein encoded by this gene is characterized by the presence of multiple copies of DUF4098 near its C-terminus. It is described as a Long Interspersed Nuclear Element (LINE), a subclass of penaeid repetitive elements (PREs).
C8orf48 is a protein that in humans is encoded by the C8orf48 gene. C8orf48 is a nuclear protein specifically predicted to be located in the nuclear lamina. C8orf48 has been found to interact with proteins that are involved in the regulation of various cellular responses like gene expression, protein secretion, cell proliferation, and inflammatory responses. This protein has been linked to breast cancer and papillary thyroid carcinoma.
Coiled-coil domain containing protein 180 (CCDC180) is a protein that in humans is encoded by the CCDC180 gene. This protein is known to localize to the nucleus and is thought to be involved in regulation of transcription as are many proteins containing coiled-coil domains. As it is expressed most highly in the testes and is regulated by SRY and SOX transcription factors, it could be involved in sex determination.
Transmembrane Protein 176B, or TMEM176B is a transmembrane protein that in humans is encoded by the TMEM176B gene. It is thought to play a role in the process of maturation of dendritic cells.
Uncharacterized protein Chromosome 16 Open Reading Frame 71 is a protein in humans, encoded by the C16orf71 gene. The gene is expressed in epithelial tissue of the respiratory system, adipose tissue, and the testes. Predicted associated biological processes of the gene include regulation of the cell cycle, cell proliferation, apoptosis, and cell differentiation in those tissue types. 1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3, indicating the possibility of regulated alternate expression.
Uncharacterized protein C2orf73 is a protein that in humans is encoded by the C2orf73 gene. The protein is predicted to be localized to the nucleus.
Testis-expressed protein 9 is a protein that in humans is encoded the TEX9 gene. TEX9 that encodes a 391-long amino acid protein containing two coiled-coil regions. The gene is conserved in many species and encodes orthologous proteins in eukarya, archaea, and one species of bacteria. The function of TEX9 is not yet fully understood, but it is suggested to have ATP-binding capabilities.
Uncharacterized protein C16orf86 is a protein in humans that is encoded by the C16orf86 gene. It is mostly made of alpha helices and it is expressed in the testes, but also in other tissues such as the kidney, colon, brain, fat, spleen, and liver. For the function of C16orf86, it is not well understood, however it could be a transcription factor in the nucleus that regulates G0/G1 in the cell cycle for tissues such as the kidney, brain, and skeletal muscles as mentioned in the DNA microarray data below in the gene level regulation section.
Cilia- and flagella-associated protein 299 (CFAP299), is a protein that in humans is encoded by the CFAP299 gene. CFAP299 is predicted to play a role in spermatogenesis and cell apoptosis.
FAM71E2, also known as Family With Sequence Similarity 71 Member E2, is a protein that, in humans, is encoded by the FAM71E2 gene. Aliases include C19orf16, Protein FAM71E2, Chromosome 19 open reading frame 16, and Putative Protein FAM71E2. The gene is primarily conserved in mammals, but it is also conserved in two reptile species.
Chromosome 1 open reading frame 141, or C1orf141 is a protein which, in humans, is encoded by gene C1orf141. It is a precursor protein that becomes active after cleavage. The function is not yet well understood, but it is suggested to be active during development
Transmembrane protein 179 is a protein that in humans is encoded by the TMEM179 gene. The function of transmembrane protein 179 is not yet well understood, but it is believed to have a function in the nervous system.
Chromosome 1 Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood.
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.
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.
Synaptosome-associated protein, 47 kDal (SNAP47) is a human protein encoded by the SNAP47 gene. Other aliases of this gene are SVAP1, HEL170, ESFI5812, and HEL-S-290. SNAP47 is a synaptosome protein which is associated with the protein coding in multiple diseases, including non small cell lung cancer and schizophrenia. SNAP47 is a member of the SNAP protein family. SNAP proteins are t-snare proteins that are a component of SNARE complex. The SNARE complex mediates vesicle fusion by creating tight complex that brings vesicle and membrane together. This protein causes ubiquitous expression in testis, ovary, and many other tissues
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.
Family with Sequence Similarity 166, member C (FAM166C), is a protein encoded by the FAM166C gene. The protein FAM166C is localized in the nucleus. It has a calculated molecular weight of 23.29 kDa. It also contains DUF2475, a protein of unknown function from amino acid 19–85. The FAM166C protein is nominally expressed in the testis, stomach, and thyroid.
Chromosome 5 open reading frame 22 (c5orf22) is a protein-coding gene of poorly characterized function in Homo sapiens. The primary alias is unknown protein family 0489 (UPF0489).
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