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
//