YIF1A
Protein YIF1A is a protein that in humans is encoded by the YIF1A gene[1]
Gene
editGeneral properties
editYIF1A (Yip1 interacting factor homolog A) is also known as YIF1, YIF1P, FinGER7, and 54TM.[2] 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.[1]
Promoters
editThe predicted promoter region (GXP_50494) is 1252 base pairs long and extends past the first exon of YIF1A.[3] Transcription factors predicted to bind to the promoter region include GATA-binding factor, E2F transcription factor 1, X-box binding protein RFX1, zinc finger protein 64 (ZNF338), and transcriptional repressor CDP.
Expression
editThe 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. [4][5][6] 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.
mRNA
editYIF1A has isoforms 1 and 2, with exons 8 and 7 respectively.[1] The two transcripts undergo alternate splicing and are translated into proteins with 293 and 241 amino acids, respectively.[7][8]
RNA-binding proteins
editThe 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.[9]
Protein
editGeneral Properties
editThe 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.[8][10][11]
Composition
editYIF1 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.[10]
Domain and motifs
editYIF1A has a conserved domain, pfam03878 (AA 57 →287).[1]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. [2]
Structure
editThe structure of YIF1A consists of approximately 59% alpha-helices, with TM helix and disordered regions making up the rest of the structure; no beta- strand was predicted.[14]
Localization
editYIF1A's predicted location is in the endoplasmic reticulum, with intracellular N-terminus and an extracellular C-terminus.[15][16]
Post-translational modifications
editYIF1A undergoes methionine cleavage and N-terminal acetylation, which is one of the most common post translation modifications of eukaryotic proteins.[17]It also phosphorylated by unspecified kinases at several sites.[18] Three glycation site is predicted in lysine residue(lys 104,161, and 211).[19] YIF1A undergoes O-ß-GlcNAc modification at 5 sites, 1 of them being Yin-Yang sites. [20]
Interacting protein
editBased 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.[21] It also participates in ER unfolded protein response (UPR) by inducing ERN1/IRE1.[22]
Homology
editYIF1A has a single Paralog called YIF1B, which is located on human chromosome 19.[2]YIF1A has 238 identified orthologs.[23] 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 | Acession Number | Date of Divergence (MYA)[24] | Sequence Length( | Sequence Identity[25] |
---|---|---|---|---|
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 |
Reference
edit- ^ a b c d "YIF1A - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-06-21.
- ^ a b c "YIF1A related genes - GeneCards Search Results". www.genecards.org. Retrieved 2020-06-21.
- ^ "Genomatix: Genome Annotation and Browser: Query Input". www.genomatix.de. Retrieved 2020-07-30.
- ^ Fagerberg, Linn; Hallström, Björn M.; Oksvold, Per; Kampf, Caroline; Djureinovic, Dijana; Odeberg, Jacob; Habuka, Masato; Tahmasebpoor, Simin; Danielsson, Angelika; Edlund, Karolina; Asplund, Anna (2014-02-14). "Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics". Molecular & cellular proteomics: MCP. 13 (2): 397–406. doi:10.1074/mcp.M113.035600. ISSN 1535-9484. PMC 3916642. PMID 24309898.
{{cite journal}}
: CS1 maint: unflagged free DOI (link) - ^ Duff, Michael O.; Olson, Sara; Wei, Xintao; Garrett, Sandra C.; Osman, Ahmad; Bolisetty, Mohan; Plocik, Alex; Celniker, Susan E.; Graveley, Brenton R. (2015-05-21). "Genome-wide identification of zero nucleotide recursive splicing in Drosophila". Nature. 521 (7552): 376–379. doi:10.1038/nature14475. ISSN 1476-4687. PMC 4529404. PMID 25970244.
- ^ Szabo, Linda; Morey, Robert; Palpant, Nathan J.; Wang, Peter L.; Afari, Nastaran; Jiang, Chuan; Parast, Mana M.; Murry, Charles E.; Laurent, Louise C.; Salzman, Julia (2015-06-16). "Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development". Genome Biology. 16: 126. doi:10.1186/s13059-015-0690-5. ISSN 1474-760X. PMC 4506483. PMID 26076956.
{{cite journal}}
: CS1 maint: unflagged free DOI (link) - ^ "protein YIF1A isoform 2 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-07-28.
- ^ a b "protein YIF1A isoform 1 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-07-28.
- ^ "RBPDB: The database of RNA-binding specificities". rbpdb.ccbr.utoronto.ca. Retrieved 2020-08-01.
- ^ a b "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2020-07-28.
- ^ "ExPASy - Compute pI/Mw tool". web.expasy.org. Retrieved 2020-07-28.
- ^ "I-TASSER server for protein structure and function prediction". zhanglab.ccmb.med.umich.edu. Retrieved 2020-08-01.
- ^ "iCn3D: Web-based 3D Structure Viewer". www.ncbi.nlm.nih.gov. Retrieved 2020-08-01.
- ^ "NPS@ : GOR4 secondary structure prediction". npsa-prabi.ibcp.fr. Retrieved 2020-07-28.
- ^ "PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features". www.predictprotein.org. Retrieved 2020-07-28.
- ^ "Phobius". phobius.sbc.su.se. Retrieved 2020-07-28.
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- ^ Kuijpers, Marijn; Yu, Ka Lou; Teuling, Eva; Akhmanova, Anna; Jaarsma, Dick; Hoogenraad, Casper C. (2013-07-17). "The ALS8 protein VAPB interacts with the ER-Golgi recycling protein YIF1A and regulates membrane delivery into dendrites". The EMBO journal. 32 (14): 2056–2072. doi:10.1038/emboj.2013.131. ISSN 1460-2075. PMC 3715857. PMID 23736259.
- ^ "YIF1A protein (human) - STRING interaction network". string-db.org. Retrieved 2020-07-29.
- ^ "Nucleotide BLAST: Search nucleotide databases using a nucleotide query". blast.ncbi.nlm.nih.gov. Retrieved 2020-08-01.
- ^ "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2020-07-02.
- ^ "Human BLAT Search". genome.ucsc.edu. Retrieved 2020-07-02.