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Database: UniProt
Entry: Q9YHX5_DANRE
LinkDB: Q9YHX5_DANRE
Original site: Q9YHX5_DANRE 
ID   Q9YHX5_DANRE            Unreviewed;       455 AA.
AC   Q9YHX5;
DT   01-MAY-1999, integrated into UniProtKB/TrEMBL.
DT   01-MAY-1999, sequence version 1.
DT   24-JAN-2024, entry version 167.
DE   SubName: Full=Vimentin {ECO:0000313|EMBL:AAC98491.1, ECO:0000313|RefSeq:NP_571947.1};
GN   Name=cb28 {ECO:0000313|RefSeq:NP_571947.1};
GN   OrderedLocusNames=vim {ECO:0000313|EMBL:AAH53115.1,
GN   ECO:0000313|RefSeq:NP_571947.1, ECO:0000313|ZFIN:ZDB-GENE-011212-3};
OS   Danio rerio (Zebrafish) (Brachydanio rerio).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC   Danionidae; Danioninae; Danio.
OX   NCBI_TaxID=7955 {ECO:0000313|EMBL:AAC98491.1};
RN   [1] {ECO:0000313|EMBL:AAH53115.1}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Embryo {ECO:0000313|EMBL:AAH53115.1};
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=16109975;
RA   Woods I.G., Wilson C., Friedlander B., Chang P., Reyes D.K., Nix R.,
RA   Kelly P.D., Chu F., Postlethwait J.H., Talbot W.S.;
RT   "The zebrafish gene map defines ancestral vertebrate chromosomes.";
RL   Genome Res. 15:1307-1314(2005).
RN   [3] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=16379021;
RA   Vihtelic T.S., Fadool J.M., Gao J., Thornton K.A., Hyde D.R., Wistow G.;
RT   "Expressed sequence tag analysis of zebrafish eye tissues for NEIBank.";
RL   Mol. Vis. 11:1083-1100(2005).
RN   [4] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=17565703;
RA   Kassen S.C., Ramanan V., Montgomery J.E., T Burket C., Liu C.G.,
RA   Vihtelic T.S., Hyde D.R.;
RT   "Time course analysis of gene expression during light-induced photoreceptor
RT   cell death and regeneration in albino zebrafish.";
RL   Dev. Neurobiol. 67:1009-1031(2007).
RN   [5] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=18550893; DOI=10.1074/mcp.m800081-mcp200;
RA   Lemeer S., Jopling C., Gouw J., Mohammed S., Heck A.J., Slijper M.,
RA   den Hertog J.;
RT   "Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown
RT   embryos.";
RL   Mol. Cell. Proteomics 7:2176-2187(2008).
RN   [6] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=19936306;
RA   Greiling T.M., Houck S.A., Clark J.I.;
RT   "The zebrafish lens proteome during development and aging.";
RL   Mol. Vis. 15:2313-2325(2009).
RN   [7] {ECO:0000313|Proteomes:UP000000437}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=23594743; DOI=10.1038/nature12111;
RG   Genome Reference Consortium Zebrafish;
RA   Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA   Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA   Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA   White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA   Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA   Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA   Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA   Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA   Clee C., Oliver K., Clark R., Riddle C., Elliot D., Eliott D.,
RA   Threadgold G., Harden G., Ware D., Begum S., Mortimore B., Mortimer B.,
RA   Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M.,
RA   Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M.,
RA   Glithero R., Howden P., Barker N., Lloyd C., Stevens C., Harley J.,
RA   Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D.,
RA   Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K.,
RA   Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R.,
RA   Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M.,
RA   Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D.,
RA   Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M.,
RA   Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M.,
RA   Woodmansey R., Clark G., Cooper J., Cooper J., Tromans A., Grafham D.,
RA   Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J.,
RA   Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I.,
RA   Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
RA   Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
RA   Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G., Osoegawa K., Zhu B.,
RA   Rapp A., Widaa S., Langford C., Yang F., Schuster S.C., Carter N.P.,
RA   Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R.,
RA   Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I.,
RA   Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H.,
RA   Rogers J., Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the human
RT   genome.";
RL   Nature 496:498-503(2013).
RN   [8] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=30449506;
RA   Anbalagan S., Gordon L., Blechman J., Matsuoka R.L., Rajamannar P.,
RA   Wircer E., Biran J., Reuveny A., Leshkowitz D., Stainier D.Y.R.,
RA   Levkowitz G.;
RT   "Pituicyte Cues Regulate the Development of Permeable Neuro-Vascular
RT   Interfaces.";
RL   Dev. Cell 47:711-726(2018).
RN   [9] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=30258730;
RA   Ranski A.H., Kramer A.C., Morgan G.W., Perez J.L., Thummel R.;
RT   "Characterization of retinal regeneration in adult zebrafish following
RT   multiple rounds of phototoxic lesion.";
RL   PeerJ 6:e5646-e5646(2018).
RN   [10] {ECO:0000313|EMBL:AAC98491.1}
RP   NUCLEOTIDE SEQUENCE.
RA   Quirk P.G., Krulwich T.A.;
RL   Submitted (JUL-2018) to the EMBL/GenBank/DDBJ databases.
RN   [11] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=31042481;
RA   Xue Y., Liu D., Cui G., Ding Y., Ai D., Gao S., Zhang Y., Suo S., Wang X.,
RA   Lv P., Zhou C., Li Y., Chen X., Peng G., Jing N., Han J.J., Liu F.;
RT   "A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-
RT   dimensional RNA-Seq Analysis.";
RL   Cell Rep. 27:1567-1578(2019).
RN   [12] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=30890583; DOI=10.1242/dmm.037390;
RA   Brilli Skvarca L., Han H.I., Espiritu E.B., Missinato M.A., Rochon E.R.,
RA   McDaniels M.D., Bais A.S., Roman B.L., Waxman J.S., Watkins S.C.,
RA   Davidson A.J., Tsang M., Hukriede N.A.;
RT   "Enhancing regeneration after acute kidney injury by promoting cellular
RT   dedifferentiation in zebrafish. .";
RL   Dis. Model. Mech. 12:dmm037390-dmm037390(2019).
RN   [13] {ECO:0000313|RefSeq:NP_571947.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=30387501;
RA   Liao M.L., Peng W.H., Kan D., Chien C.L.;
RT   "Distribution patterns of the zebrafish neuronal intermediate filaments
RT   inaa and inab.";
RL   J. Neurosci. Res. 97:202-214(2019).
RN   [14] {ECO:0000313|RefSeq:NP_571947.1}
RP   IDENTIFICATION.
RG   RefSeq;
RL   Submitted (SEP-2023) to UniProtKB.
CC   -!- FUNCTION: Vimentins are class-III intermediate filaments found in
CC       various non-epithelial cells, especially mesenchymal cells. Vimentin is
CC       attached to the nucleus, endoplasmic reticulum, and mitochondria,
CC       either laterally or terminally. {ECO:0000256|ARBA:ARBA00002825}.
CC   -!- SIMILARITY: Belongs to the intermediate filament family.
CC       {ECO:0000256|RuleBase:RU000685}.
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DR   EMBL; AF069994; AAC98491.1; -; mRNA.
DR   EMBL; BC053115; AAH53115.1; -; mRNA.
DR   RefSeq; NP_571947.1; NM_131872.2.
DR   GeneID; 140599; -.
DR   KEGG; dre:140599; -.
DR   CTD; 7431; -.
DR   ZFIN; ZDB-GENE-011212-3; vim.
DR   OrthoDB; 4640531at2759; -.
DR   Proteomes; UP000000437; Chromosome 24.
DR   GO; GO:0030424; C:axon; IBA:GO_Central.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005882; C:intermediate filament; IBA:GO_Central.
DR   GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR   GO; GO:0005200; F:structural constituent of cytoskeleton; IBA:GO_Central.
DR   GO; GO:0045109; P:intermediate filament organization; IBA:GO_Central.
DR   GO; GO:0042060; P:wound healing; IMP:ZFIN.
DR   Gene3D; 1.20.5.170; -; 1.
DR   Gene3D; 1.20.5.500; Single helix bin; 1.
DR   Gene3D; 1.20.5.1160; Vasodilator-stimulated phosphoprotein; 1.
DR   InterPro; IPR018039; IF_conserved.
DR   InterPro; IPR039008; IF_rod_dom.
DR   InterPro; IPR006821; Intermed_filament_DNA-bd.
DR   PANTHER; PTHR45652; GLIAL FIBRILLARY ACIDIC PROTEIN; 1.
DR   PANTHER; PTHR45652:SF5; VIMENTIN; 1.
DR   Pfam; PF00038; Filament; 1.
DR   Pfam; PF04732; Filament_head; 1.
DR   SMART; SM01391; Filament; 1.
DR   SUPFAM; SSF64593; Intermediate filament protein, coiled coil region; 2.
DR   PROSITE; PS00226; IF_ROD_1; 1.
DR   PROSITE; PS51842; IF_ROD_2; 1.
PE   1: Evidence at protein level;
KW   Coiled coil {ECO:0000256|ARBA:ARBA00023054, ECO:0000256|SAM:Coils};
KW   Intermediate filament {ECO:0000256|ARBA:ARBA00022754,
KW   ECO:0000256|RuleBase:RU000685};
KW   Proteomics identification {ECO:0007829|PeptideAtlas:Q9YHX5};
KW   Reference proteome {ECO:0000313|Proteomes:UP000000437}.
FT   DOMAIN          94..402
FT                   /note="IF rod"
FT                   /evidence="ECO:0000259|PROSITE:PS51842"
FT   REGION          1..45
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COILED          84..235
FT                   /evidence="ECO:0000256|SAM:Coils"
FT   COILED          293..380
FT                   /evidence="ECO:0000256|SAM:Coils"
FT   COMPBIAS        23..45
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   455 AA;  52508 MW;  53470B01B8816EAF CRC64;
     MASRTSTSSY KRMFGGERPA AARSTFSSRQ YSSPVRVSSS RTSYNYSSAP PSVYASKGLR
     VRSGAPLPRL ATDTLDFGLA EAINTEFKAN RTNEKAEMQH LNDRFASYID KVRFLEQQNK
     ILIAELEQLR GKGASRVGDL YEDEMRELRR QVDQLTGEKS KVEVDRDNLG EDIERLKERL
     QEEMLQREDA ENSLRSFRQD VDNASLARLD LERKVESLQE EIAFLKKLHD EELAEMQIQM
     QEQHLQIDME VTKPDLTAAL KDVRQQYETL ASRNLQESED WYKSKFADLS EAAARNNEAI
     RLAKQEANDY RRQLQALTCD LEALKGTNES LERQMRELED SFSMEASGYQ DTIGRLEDDI
     RNMKDEMARH LREYQDLLNV KMALDIEIAT YRKLLEGEES RITSPFPNFS SLSLRESMKE
     TRPLIDNLSK KVVIKTIETR DGHIINESTQ NEDLE
//
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