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YIF1A

Protein YIF1A is a protein that in humans is encoded by the YIF1A gene[1]

Gene

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General properties

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YIF1A (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

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The 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

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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. [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

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YIF1A 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

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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.[9]

Protein

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General Properties

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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.[8][10][11]

 
Schematic illustration of YIF1A, with domains and post-translation modifications.

Composition

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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.[10]

Domain and motifs

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YIF1A 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

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YIF1A protein structure generated by I-Tasser and visualized with iCn3D.[12][13] Transmembrane domains are red, non-cytosolic domains are yellow, and cytosolic domains are deep pink.

The 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

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YIF1A's predicted location is in the endoplasmic reticulum, with intracellular N-terminus and an extracellular C-terminus.[15][16]

Post-translational modifications

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YIF1A 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

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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.[21] It also participates in ER unfolded protein response (UPR) by inducing ERN1/IRE1.[22]

 
Conceptual translation of Hsa_YIF1A transcript variant 1, mRNA (NM 020470)


Homology

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YIF1A 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

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  1. ^ a b c d "YIF1A - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-06-21.
  2. ^ a b c "YIF1A related genes - GeneCards Search Results". www.genecards.org. Retrieved 2020-06-21.
  3. ^ "Genomatix: Genome Annotation and Browser: Query Input". www.genomatix.de. Retrieved 2020-07-30.
  4. ^ 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)
  5. ^ 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.
  6. ^ 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)
  7. ^ "protein YIF1A isoform 2 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-07-28.
  8. ^ a b "protein YIF1A isoform 1 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2020-07-28.
  9. ^ "RBPDB: The database of RNA-binding specificities". rbpdb.ccbr.utoronto.ca. Retrieved 2020-08-01.
  10. ^ a b "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2020-07-28.
  11. ^ "ExPASy - Compute pI/Mw tool". web.expasy.org. Retrieved 2020-07-28.
  12. ^ "I-TASSER server for protein structure and function prediction". zhanglab.ccmb.med.umich.edu. Retrieved 2020-08-01.
  13. ^ "iCn3D: Web-based 3D Structure Viewer". www.ncbi.nlm.nih.gov. Retrieved 2020-08-01.
  14. ^ "NPS@ : GOR4 secondary structure prediction". npsa-prabi.ibcp.fr. Retrieved 2020-07-28.
  15. ^ "PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features". www.predictprotein.org. Retrieved 2020-07-28.
  16. ^ "Phobius". phobius.sbc.su.se. Retrieved 2020-07-28.
  17. ^ "TERMINUS - Welcome to terminus". terminus.unige.ch. Retrieved 2020-07-28.
  18. ^ "NetPhosK 1.0 Server". www.cbs.dtu.dk. Retrieved 2020-07-28.
  19. ^ "NetGlycate 1.0 Server - prediction results". www.cbs.dtu.dk. Retrieved 2020-08-01.
  20. ^ "YinOYang 1.2 Server". www.cbs.dtu.dk. Retrieved 2020-07-28.
  21. ^ 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.
  22. ^ "YIF1A protein (human) - STRING interaction network". string-db.org. Retrieved 2020-07-29.
  23. ^ "Nucleotide BLAST: Search nucleotide databases using a nucleotide query". blast.ncbi.nlm.nih.gov. Retrieved 2020-08-01.
  24. ^ "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2020-07-02.
  25. ^ "Human BLAT Search". genome.ucsc.edu. Retrieved 2020-07-02.
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