ID   NRF1_DANRE              Reviewed;         514 AA.
AC   Q90X44; O93570; Q7ZTS6;
DT   27-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT   27-JUN-2006, sequence version 2.
DT   03-AUG-2022, entry version 119.
DE   RecName: Full=Nuclear respiratory factor 1;
DE            Short=Nrf-1;
DE   AltName: Full=Not really finished protein;
GN   Name=nrf1;
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] (ISOFORM 2), FUNCTION, AND DEVELOPMENTAL STAGE.
RC   TISSUE=Embryo;
RX   PubMed=9778497; DOI=10.1242/dev.125.22.4369;
RA   Becker T.S., Burgess S.M., Amsterdam A.H., Allende M.L., Hopkins N.H.;
RT   "Not really finished is crucial for development of the zebrafish outer
RT   retina and encodes a transcription factor highly homologous to human
RT   nuclear respiratory factor-1 and avian initiation binding repressor.";
RL   Development 125:4369-4378(1998).
RN   [2]
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).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC   STRAIN=AB;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Probable transcription factor that is required for normal
CC       development of the outer retina. {ECO:0000269|PubMed:9778497}.
CC   -!- SUBUNIT: Homodimer. Binds DNA as a dimer (By similarity).
CC       {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q90X44-2; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q90X44-1; Sequence=VSP_019575;
CC   -!- DEVELOPMENTAL STAGE: Expressed in the developing eye and CNS prior to
CC       neuronal differentiation. First detected at around 18 hours post-
CC       fertilization (hpf) in the eye primordia and brain. At 24-42 hpf,
CC       expressed in most cells of the developing eyes, CNS and ears. At 48
CC       hpf, also detected in the optic nerve and tracts. By 56 hpf, levels are
CC       barely detectable. {ECO:0000269|PubMed:9778497}.
CC   -!- SIMILARITY: Belongs to the NRF1/Ewg family. {ECO:0000305}.
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DR   EMBL; AF087671; AAC36478.1; -; mRNA.
DR   EMBL; AL590150; CAC94898.1; -; Genomic_DNA.
DR   EMBL; BC044537; AAH44537.1; -; mRNA.
DR   RefSeq; NP_001315469.1; NM_001328540.1. [Q90X44-2]
DR   RefSeq; NP_571755.2; NM_131680.2. [Q90X44-1]
DR   AlphaFoldDB; Q90X44; -.
DR   STRING; 7955.ENSDARP00000000019; -.
DR   PaxDb; Q90X44; -.
DR   Ensembl; ENSDART00000138183; ENSDARP00000116798; ENSDARG00000000018. [Q90X44-1]
DR   Ensembl; ENSDART00000181044; ENSDARP00000149440; ENSDARG00000000018. [Q90X44-2]
DR   GeneID; 64604; -.
DR   KEGG; dre:64604; -.
DR   CTD; 4899; -.
DR   ZFIN; ZDB-GENE-001221-1; nrf1.
DR   eggNOG; ENOG502QTK1; Eukaryota.
DR   GeneTree; ENSGT00390000006835; -.
DR   HOGENOM; CLU_018156_3_1_1; -.
DR   InParanoid; Q90X44; -.
DR   OMA; EVEPSWA; -.
DR   OrthoDB; 858632at2759; -.
DR   PhylomeDB; Q90X44; -.
DR   TreeFam; TF105308; -.
DR   PRO; PR:Q90X44; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 4.
DR   Bgee; ENSDARG00000000018; Expressed in cleaving embryo and 39 other tissues.
DR   GO; GO:0005634; C:nucleus; ISS:AgBase.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR   GO; GO:0042803; F:protein homodimerization activity; ISS:AgBase.
DR   GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; ISS:AgBase.
DR   GO; GO:0070417; P:cellular response to cold; IDA:ZFIN.
DR   GO; GO:0003407; P:neural retina development; IMP:UniProtKB.
DR   GO; GO:0045494; P:photoreceptor cell maintenance; IMP:ZFIN.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR   GO; GO:0014823; P:response to activity; IDA:ZFIN.
DR   GO; GO:0060041; P:retina development in camera-type eye; IMP:ZFIN.
DR   GO; GO:0001895; P:retina homeostasis; IMP:ZFIN.
DR   InterPro; IPR039142; NRF1/Ewg.
DR   InterPro; IPR019526; Nrf1_activation-bd.
DR   InterPro; IPR019525; Nrf1_NLS/DNA-bd_dimer.
DR   PANTHER; PTHR20338; PTHR20338; 1.
DR   Pfam; PF10492; Nrf1_activ_bdg; 1.
DR   Pfam; PF10491; Nrf1_DNA-bind; 1.
PE   2: Evidence at transcript level;
KW   Activator; Alternative splicing; Developmental protein; DNA-binding;
KW   Nucleus; Reference proteome; Transcription; Transcription regulation.
FT   CHAIN           1..514
FT                   /note="Nuclear respiratory factor 1"
FT                   /id="PRO_0000100211"
FT   DNA_BIND        109..307
FT                   /evidence="ECO:0000250"
FT   REGION          1..78
FT                   /note="Dimerization"
FT                   /evidence="ECO:0000250"
FT   REGION          38..61
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          303..488
FT                   /note="Required for transcriptional activation"
FT                   /evidence="ECO:0000250"
FT   MOTIF           88..116
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         410..420
FT                   /note="RYSLEGALKFG -> S (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:9778497"
FT                   /id="VSP_019575"
FT   CONFLICT        157
FT                   /note="R -> G (in Ref. 3; AAH44537)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        302
FT                   /note="L -> P (in Ref. 1; AAC36478)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        399
FT                   /note="Q -> R (in Ref. 1; AAC36478)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   514 AA;  54708 MW;  77AC284C73276650 CRC64;
     MEDHTVHQTE HMTTIEAHAV SQQVGQVHVA TYTEHGMLSA DEDSPSSPDD DAYDDSDILN
     STGTDEVTAH LAAAGPVGMA AAAAVATGKK RKRPHIFESN PSIRKRQQTR LLRKLRATLD
     EYTTRVGQQA IVLCISPSKP NPVFRVFGAA PLENVVRKYK SMILEDLENA LAEHAPPGGG
     ELSSELPPLT IDGIPVSVDK MTQAQLRAFI PEMLKYSTGR GKPGWGKESC KPIWWPEDIP
     WANVRSDVRT EEQKQRVSWT QALRTIVKNC YKQHGREDLL YAFEDQVTTQ VATTATHSIA
     HLVPSQTVVQ TISNPDGTVS LIQVGTGATV ATLADASELP GTVTVAQVNY STVTDGEVEQ
     NWATLQGGEM TIQTTQASEA TQAVASLAEA AVAASQEMQT GATVTMALNR YSLEGALKFG
     EAAAHAVATL AEATLQGGGQ IVLAGETAAA VGALTGVPDG SGLVQIPVSM YQTVVTSLAQ
     GNRPVQVAMA PVTTRIDNTM TLDGQAVEVV TLEQ