RFX4_DANRE
ID RFX4_DANRE Reviewed; 735 AA.
AC A2BGA0; A7M781; Q6YM51;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 20-FEB-2007, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Transcription factor RFX4;
DE AltName: Full=Regulatory factor X 4;
GN Name=rfx4; ORFNames=si:dkey-103i16.7;
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;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=12925582; DOI=10.1242/dev.00661;
RA Blackshear P.J., Graves J.P., Stumpo D.J., Cobos I., Rubenstein J.L.R.,
RA Zeldin D.C.;
RT "Graded phenotypic response to partial and complete deficiency of a brain-
RT specific transcript variant of the winged helix transcription factor
RT RFX4.";
RL Development 130:4539-4552(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=18065431; DOI=10.1242/dev.009050;
RA Nagayoshi S., Hayashi E., Abe G., Osato N., Asakawa K., Urasaki A.,
RA Horikawa K., Ikeo K., Takeda H., Kawakami K.;
RT "Insertional mutagenesis by the Tol2 transposon-mediated enhancer trap
RT approach generated mutations in two developmental genes: tcf7 and
RT synembryn-like.";
RL Development 135:159-169(2008).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
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., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., 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).
CC -!- FUNCTION: May activate transcription by interacting directly with the
CC X-box. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00858}.
CC -!- SIMILARITY: Belongs to the RFX family. {ECO:0000255|PROSITE-
CC ProRule:PRU00858}.
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DR EMBL; AY102011; AAM52486.1; -; mRNA.
DR EMBL; AB355649; BAF75865.1; -; mRNA.
DR EMBL; BX465207; CAM12990.1; -; Genomic_DNA.
DR RefSeq; NP_991275.1; NM_205712.1.
DR AlphaFoldDB; A2BGA0; -.
DR SMR; A2BGA0; -.
DR STRING; 7955.ENSDARP00000032295; -.
DR PaxDb; A2BGA0; -.
DR PeptideAtlas; A2BGA0; -.
DR Ensembl; ENSDART00000031752; ENSDARP00000032295; ENSDARG00000026395.
DR GeneID; 403016; -.
DR KEGG; dre:403016; -.
DR CTD; 5992; -.
DR ZFIN; ZDB-GENE-040909-2; rfx4.
DR eggNOG; KOG3712; Eukaryota.
DR GeneTree; ENSGT01050000244879; -.
DR HOGENOM; CLU_377067_0_0_1; -.
DR InParanoid; A2BGA0; -.
DR OMA; YQLNSQM; -.
DR OrthoDB; 346630at2759; -.
DR PhylomeDB; A2BGA0; -.
DR TreeFam; TF321340; -.
DR PRO; PR:A2BGA0; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 18.
DR Bgee; ENSDARG00000026395; Expressed in embryo and 8 other tissues.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0021914; P:negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0007418; P:ventral midline development; IMP:ZFIN.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR003150; DNA-bd_RFX.
DR InterPro; IPR039779; RFX-like.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR PANTHER; PTHR12619; PTHR12619; 1.
DR Pfam; PF02257; RFX_DNA_binding; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR PROSITE; PS51526; RFX_DBD; 1.
PE 2: Evidence at transcript level;
KW Activator; DNA-binding; Nucleus; Reference proteome; Transcription;
KW Transcription regulation.
FT CHAIN 1..735
FT /note="Transcription factor RFX4"
FT /id="PRO_0000314239"
FT DNA_BIND 44..126
FT DNA_BIND 61..136
FT /note="RFX-type winged-helix"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00858"
FT REGION 25..59
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 315..487
FT /note="Necessary for dimerization"
FT CONFLICT 2
FT /note="H -> L (in Ref. 1; AAM52486)"
FT /evidence="ECO:0000305"
FT CONFLICT 40
FT /note="S -> P (in Ref. 2; BAF75865)"
FT /evidence="ECO:0000305"
FT CONFLICT 80
FT /note="S -> I (in Ref. 1; AAM52486)"
FT /evidence="ECO:0000305"
FT CONFLICT 214
FT /note="D -> G (in Ref. 2; BAF75865)"
FT /evidence="ECO:0000305"
FT CONFLICT 446
FT /note="S -> G (in Ref. 2; BAF75865)"
FT /evidence="ECO:0000305"
FT CONFLICT 510
FT /note="A -> G (in Ref. 1; AAM52486)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 735 AA; 82819 MW; 035F2C6FDAEDD073 CRC64;
MHCGLLEEPD MDSTESWIER CLNESESKRF SSHSSIGNIS NDENEEKENN RASKPHSTPA
TLQWLEENYE IAEGVCIPRS ALYMHYLDFC EKLDSQPVNA ASFGKIIRQQ FPQLTTRRLG
TRGQSKYHYY GIAVKESSQY YDVMYSKKGA AWVNETGKKE VTKQTVAYSP RSKLGTLLPD
FPNVKDLNLP ASLPEEKVST FIMMYRTHCQ RILDTVIRAN FDEVQSFLLH FWQGMPPHML
PVLGSSTVVN IVGVCDSILY KAISGVLMPT VLQALPDSLT QVIRKFAKQL DEWLKVALHD
LPENLRNIKF ELSRRFSQIL KRQTSLNHLC QASRTVIHSA DITFQMLEDW RNVDLNSITK
QTLYTMEDSR EDQRRLIIQL YQEFDRLLED QSPIEAYIEW LDSMVERCVV RVAGKRPGSL
KRVAQQFLLM WSCFGTRVIR DMTLHSAPSF GSFHLIHLMF DDYVLYLLES LHCQERANEL
MRAMKGEGAP ADTGEELMLM SSTPTSTSPA PYSPAKSVHS VGVPAVGSPN SAQSPEYTSI
SATTGAVQSY TWSLTYTVTT SGGSPTEPGS QLSCMRGGPA LHGSSSAHRM PVYPHRDEHG
YTGSYNYSSY ANQHHHAIQS QYSSLTHEAG LPTPLHYSSY HRTSAQYPLN SQMSRMESCL
MSGSPLLHSS PVTPRWPDVP SANSCYSSPT VHASRYSTGD MYSPLAPRRN SEYEHAQHFP
GFAYINGEAT TGWAK
