ID Q6P6Y4_DANRE Unreviewed; 502 AA.
AC Q6P6Y4; A0A8M1PHZ9;
DT 05-JUL-2004, integrated into UniProtKB/TrEMBL.
DT 05-JUL-2004, sequence version 1.
DT 24-JAN-2024, entry version 125.
DE SubName: Full=RAB guanine nucleotide exchange factor (GEF) 1 {ECO:0000313|Ensembl:ENSDARP00000016779};
DE SubName: Full=Rab5 GDP/GTP exchange factor {ECO:0000313|RefSeq:NP_957137.1};
DE SubName: Full=Zgc:65944 {ECO:0000313|EMBL:AAH61953.1};
GN Name=zgc:65944 {ECO:0000313|EMBL:AAH61953.1,
GN ECO:0000313|RefSeq:NP_957137.1};
GN OrderedLocusNames=rabgef1 {ECO:0000313|Ensembl:ENSDARP00000016779,
GN ECO:0000313|RefSeq:NP_957137.1,
GN ECO:0000313|ZFIN:ZDB-GENE-040426-1486};
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:AAH61953.1};
RN [1] {ECO:0000313|EMBL:AAH61953.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Kidney {ECO:0000313|EMBL:AAH61953.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (NOV-2003) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|RefSeq:NP_957137.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=15520368; DOI=10.1073/pnas.0407241101;
RA Song H.D., Sun X.J., Deng M., Zhang G.W., Zhou Y., Wu X.Y., Sheng Y.,
RA Chen Y., Ruan Z., Jiang C.L., Fan H.Y., Zon L.I., Kanki J.P., Liu T.X.,
RA Look A.T., Chen Z.;
RT "Hematopoietic gene expression profile in zebrafish kidney marrow.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:16240-16245(2004).
RN [3] {ECO:0000313|RefSeq:NP_957137.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=19393641;
RA Ebarasi L., He L., Hultenby K., Takemoto M., Betsholtz C., Tryggvason K.,
RA Majumdar A.;
RT "A reverse genetic screen in the zebrafish identifies crb2b as a regulator
RT of the glomerular filtration barrier.";
RL Dev. Biol. 334:1-9(2009).
RN [4] {ECO:0000313|Ensembl:ENSDARP00000016779}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000016779};
RG Ensembl;
RL Submitted (FEB-2012) to UniProtKB.
RN [5] {ECO:0000313|Ensembl:ENSDARP00000016779, ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000016779};
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 [6] {ECO:0000313|RefSeq:NP_957137.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=26159098;
RA Morris J.K., Chomyk A., Song P., Parker N., Deckard S., Trapp B.D.,
RA Pimplikar S.W., Dutta R.;
RT "Decrease in levels of the evolutionarily conserved microRNA miR-124
RT affects oligodendrocyte numbers in Zebrafish, Danio rerio.";
RL Invertebr. Neurosci. 15:4-4(2015).
RN [7] {ECO:0000313|RefSeq:NP_957137.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=26469318;
RA Elkon R., Milon B., Morrison L., Shah M., Vijayakumar S., Racherla M.,
RA Leitch C.C., Silipino L., Hadi S., Weiss-Gayet M., Barras E., Schmid C.D.,
RA Ait-Lounis A., Barnes A., Song Y., Eisenman D.J., Eliyahu E.,
RA Frolenkov G.I., Strome S.E., Durand B., Zaghloul N.A., Jones S.M.,
RA Reith W., Hertzano R.;
RT "RFX transcription factors are essential for hearing in mice.";
RL Nat. Commun. 6:8549-8549(2015).
RN [8] {ECO:0000313|RefSeq:NP_957137.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=27189481;
RA Pasquier J., Cabau C., Nguyen T., Jouanno E., Severac D., Braasch I.,
RA Journot L., Pontarotti P., Klopp C., Postlethwait J.H., Guiguen Y.,
RA Bobe J.;
RT "Gene evolution and gene expression after whole genome duplication in fish:
RT the PhyloFish database.";
RL BMC Genomics 17:368-368(2016).
RN [9] {ECO:0000313|RefSeq:NP_957137.1}
RP IDENTIFICATION.
RG RefSeq;
RL Submitted (SEP-2023) to UniProtKB.
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DR EMBL; AL935293; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC061953; AAH61953.1; -; mRNA.
DR RefSeq; NP_957137.1; NM_200843.1.
DR STRING; 7955.ENSDARP00000016779; -.
DR PaxDb; 7955-ENSDARP00000112905; -.
DR Ensembl; ENSDART00000018977.7; ENSDARP00000016779.5; ENSDARG00000014430.10.
DR Ensembl; ENSDART00000138243.3; ENSDARP00000112905.1; ENSDARG00000014430.10.
DR GeneID; 393816; -.
DR KEGG; dre:393816; -.
DR CTD; 27342; -.
DR ZFIN; ZDB-GENE-040426-1486; rabgef1.
DR eggNOG; KOG2319; Eukaryota.
DR eggNOG; KOG3173; Eukaryota.
DR HOGENOM; CLU_018416_1_1_1; -.
DR OMA; PTITCAT; -.
DR OrthoDB; 20678at2759; -.
DR TreeFam; TF321331; -.
DR Reactome; R-DRE-8854214; TBC/RABGAPs.
DR Reactome; R-DRE-8876198; RAB GEFs exchange GTP for GDP on RABs.
DR Proteomes; UP000000437; Chromosome 10.
DR Bgee; ENSDARG00000014430; Expressed in early embryo and 27 other cell types or tissues.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0030139; C:endocytic vesicle; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0005085; F:guanyl-nucleotide exchange factor activity; IBA:GO_Central.
DR GO; GO:0031267; F:small GTPase binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0016192; P:vesicle-mediated transport; IEA:InterPro.
DR Gene3D; 1.10.246.120; -; 1.
DR Gene3D; 1.20.5.4770; -; 1.
DR Gene3D; 1.20.1050.80; VPS9 domain; 1.
DR InterPro; IPR041545; DUF5601.
DR InterPro; IPR003123; VPS9.
DR InterPro; IPR045046; Vps9-like.
DR InterPro; IPR037191; VPS9_dom_sf.
DR InterPro; IPR002653; Znf_A20.
DR PANTHER; PTHR23101; RAB GDP/GTP EXCHANGE FACTOR; 1.
DR PANTHER; PTHR23101:SF107; RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 1-RELATED; 1.
DR Pfam; PF18151; DUF5601; 1.
DR Pfam; PF02204; VPS9; 1.
DR Pfam; PF01754; zf-A20; 1.
DR SMART; SM00167; VPS9; 1.
DR SMART; SM00259; ZnF_A20; 1.
DR SUPFAM; SSF57716; Glucocorticoid receptor-like (DNA-binding domain); 1.
DR SUPFAM; SSF109993; VPS9 domain; 1.
DR PROSITE; PS51205; VPS9; 1.
DR PROSITE; PS51036; ZF_A20; 1.
PE 1: Evidence at protein level;
KW Coiled coil {ECO:0000256|SAM:Coils};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Proteomics identification {ECO:0007829|PeptideAtlas:Q6P6Y4};
KW Reference proteome {ECO:0000313|Proteomes:UP000000437};
KW Zinc {ECO:0000256|ARBA:ARBA00022833};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771}.
FT DOMAIN 13..47
FT /note="A20-type"
FT /evidence="ECO:0000259|PROSITE:PS51036"
FT DOMAIN 242..385
FT /note="VPS9"
FT /evidence="ECO:0000259|PROSITE:PS51205"
FT REGION 68..143
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 395..416
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 481..502
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 431..465
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 68..90
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 91..109
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 502 AA; 57410 MW; A918434F33306625 CRC64;
MSQRSERRGI HVDQSELLCK KGCGYYGNAA WQGLCSKCWR DEYQKARQRQ IQDDWALAEK
LQREEEAAYV SSHSSSQTQP PQSHSQHSLA TFSKFEEKKT NEKTRKVTTV KKFFSPSSRT
APKKESHEAK TPSPSITRQS SIETDRVSRD FVEFLKTLHK PGREIHKHSR AFIDSMGNKK
QDLSAEELSE CVQDFYQGMS DRLLNHFKGS SEKVDRVMDQ VEKYIMTRLY KSVFCPETSD
DEKKDLATQH RIRALHWVTI QMLCVPVEEE IPEVSDSVVK AITDIIEMDS KRVPRDKLAC
ITSCSKHIFN AIRVTKNEPA SADDFLPTLI YIVLKANPPR LQSNIQYITR FCNPSRLMTG
EDGYYFTNLC CAVAFIEKLD AQSLNLSPED FERYMSGQAS PRRQDDPAGW PQSGSRVNPV
LTQIQHNLSV LSSLEKRQQQ VIEGAQSLEA ELTEWQESVA REVQEILERY PLDIKPRASA
IDAENVENDR LPPPLQPQVF AG
//