ID Q8JIG3_DANRE Unreviewed; 845 AA.
AC Q8JIG3; B3DIU8; F6PCM6;
DT 01-OCT-2002, integrated into UniProtKB/TrEMBL.
DT 01-OCT-2002, sequence version 1.
DT 27-MAR-2024, entry version 161.
DE SubName: Full=BHLH-PAS transcription factor {ECO:0000313|EMBL:BAC02686.1};
DE SubName: Full=Circadian clock protein PASD1 {ECO:0000313|RefSeq:NP_840084.1, ECO:0000313|RefSeq:XP_005165177.1, ECO:0000313|RefSeq:XP_005165178.1};
DE SubName: Full=Neuronal PAS domain protein 2 {ECO:0000313|EMBL:AAI63256.1, ECO:0000313|Ensembl:ENSDARP00000016938};
GN Name=npas2 {ECO:0000313|EMBL:AAI63256.1,
GN ECO:0000313|Ensembl:ENSDARP00000016938,
GN ECO:0000313|RefSeq:NP_840084.1, ECO:0000313|RefSeq:XP_021331698.1,
GN ECO:0000313|ZFIN:ZDB-GENE-030408-3};
GN Synonyms=zfCLOCK2 {ECO:0000313|RefSeq:NP_840084.1,
GN ECO:0000313|RefSeq:XP_005165177.1, ECO:0000313|RefSeq:XP_005165178.1},
GN zfClock2 {ECO:0000313|EMBL:BAC02686.1};
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:AAI63256.1};
RN [1] {ECO:0000313|EMBL:BAC02686.1}
RP NUCLEOTIDE SEQUENCE.
RA Ishikawa T., Hirayama J., Kobayashi Y., Todo T.;
RT "CRY represses CLOCK-BMAL-mediated transcription without inhibiting DNA
RT binding of the CLOCK-BMAL heterodimer.";
RL Submitted (JUL-2002) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=15657039;
RA Appelbaum L., Anzulovich A., Baler R., Gothilf Y.;
RT "Homeobox-clock protein interaction in zebrafish. A shared mechanism for
RT pineal-specific and circadian gene expression.";
RL J. Biol. Chem. 280:11544-11551(2005).
RN [3] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=16176122;
RA Lahiri K., Vallone D., Gondi S.B., Santoriello C., Dickmeis T.,
RA Foulkes N.S.;
RT "Temperature regulates transcription in the zebrafish circadian clock.";
RL PLoS Biol. 3:e351-e351(2005).
RN [4] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=17785416;
RA Tamai T.K., Young L.C., Whitmore D.;
RT "Light signaling to the zebrafish circadian clock by Cryptochrome 1a.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:14712-14717(2007).
RN [5] {ECO:0000313|EMBL:AAI63256.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases.
RN [6] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=19147662;
RA Alon S., Eisenberg E., Jacob-Hirsch J., Rechavi G., Vatine G., Toyama R.,
RA Coon S.L., Klein D.C., Gothilf Y.;
RT "A new cis-acting regulatory element driving gene expression in the
RT zebrafish pineal gland.";
RL Bioinformatics 25:559-562(2009).
RN [7] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=19449054; DOI=10.1007/s00239-009-9232-7;
RA Wang Y., Chen K., Yao Q., Zheng X., Yang Z.;
RT "Phylogenetic analysis of zebrafish basic helix-loop-helix transcription
RT factors.";
RL J. Mol. Evol. 68:629-640(2009).
RN [8] {ECO:0000313|Ensembl:ENSDARP00000016938}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000016938};
RG Ensembl;
RL Submitted (FEB-2012) to UniProtKB.
RN [9] {ECO:0000313|Ensembl:ENSDARP00000016938, ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000016938};
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 [10] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=26950095;
RA Braasch I., Gehrke A.R., Smith J.J., Kawasaki K., Manousaki T.,
RA Pasquier J., Amores A., Desvignes T., Batzel P., Catchen J., Berlin A.M.,
RA Campbell M.S., Barrell D., Martin K.J., Mulley J.F., Ravi V., Lee A.P.,
RA Nakamura T., Chalopin D., Fan S., Wcisel D., Canestro C., Sydes J.,
RA Beaudry F.E., Sun Y., Hertel J., Beam M.J., Fasold M., Ishiyama M.,
RA Johnson J., Kehr S., Lara M., Letaw J.H., Litman G.W., Litman R.T.,
RA Mikami M., Ota T., Saha N.R., Williams L., Stadler P.F., Wang H.,
RA Taylor J.S., Fontenot Q., Ferrara A., Searle S.M., Aken B., Yandell M.,
RA Schneider I., Yoder J.A., Volff J.N., Meyer A., Amemiya C.T., Venkatesh B.,
RA Holland P.W., Guiguen Y., Bobe J., Shubin N.H., Di Palma F., Alfoldi J.,
RA Lindblad-Toh K., Postlethwait J.H.;
RT "The spotted gar genome illuminates vertebrate evolution and facilitates
RT human-teleost comparisons.";
RL Nat. Genet. 48:427-437(2016).
RN [11] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=27870848;
RA Ben-Moshe Livne Z., Alon S., Vallone D., Bayleyen Y., Tovin A., Shainer I.,
RA Nisembaum L.G., Aviram I., Smadja-Storz S., Fuentes M., Falcon J.,
RA Eisenberg E., Klein D.C., Burgess H.A., Foulkes N.S., Gothilf Y.;
RT "Genetically Blocking the Zebrafish Pineal Clock Affects Circadian
RT Behavior.";
RL PLoS Genet. 12:e1006445-e1006445(2016).
RN [12] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=28219785;
RA Liang Y.Q., Huang G.Y., Zhao J.L., Shi W.J., Hu L.X., Tian F., Liu S.S.,
RA Jiang Y.X., Ying G.G.;
RT "Transcriptional alterations induced by binary mixtures of ethinylestradiol
RT and norgestrel during the early development of zebrafish (Danio rerio).";
RL Comp. Biochem. Physiol. C Toxicol. Pharmacol. 195:60-67(2017).
RN [13] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=28832322;
RA Ciarlo C., Kaufman C.K., Kinikoglu B., Michael J., Yang S., D Amato C.,
RA Blokzijl-Franke S., den Hertog J., Schlaeger T.M., Zhou Y., Liao E.,
RA Zon L.I.;
RT "A chemical screen in zebrafish embryonic cells establishes that Akt
RT activation is required for neural crest development.";
RL Elife 6:e29145-e29145(2017).
RN [14] {ECO:0000313|RefSeq:NP_840084.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=28687631;
RA Bian S.S., Zheng X.L., Sun H.Q., Chen J.H., Lu Y.L., Liu Y.Q., Tao D.C.,
RA Ma Y.X.;
RT "Clock1a affects mesoderm development and primitive hematopoiesis by
RT regulating Nodal-Smad3 signaling in the zebrafish embryo.";
RL J. Biol. Chem. 292:14165-14175(2017).
RN [15] {ECO:0000313|Ensembl:ENSDARP00000144113}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000144113};
RG Ensembl;
RL Submitted (OCT-2017) to UniProtKB.
RN [16] {ECO:0000313|RefSeq:NP_840084.1, ECO:0000313|RefSeq:XP_005165177.1}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:XP_005165177.1,
RC ECO:0000313|RefSeq:XP_005165178.1};
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
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DR EMBL; CU464080; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC163256; AAI63256.1; -; mRNA.
DR EMBL; AB087255; BAC02686.1; -; mRNA.
DR RefSeq; NP_840084.1; NM_178299.1.
DR RefSeq; XP_005165177.1; XM_005165120.4.
DR RefSeq; XP_005165178.1; XM_005165121.4.
DR RefSeq; XP_009299565.1; XM_009301290.2.
DR RefSeq; XP_021331698.1; XM_021476023.1.
DR STRING; 7955.ENSDARP00000016938; -.
DR PaxDb; 7955-ENSDARP00000016938; -.
DR Ensembl; ENSDART00000014806.5; ENSDARP00000016938.4; ENSDARG00000016536.6.
DR Ensembl; ENSDART00000175683.2; ENSDARP00000144113.1; ENSDARG00000116993.1.
DR GeneID; 352934; -.
DR KEGG; dre:352934; -.
DR AGR; ZFIN:ZDB-GENE-030408-3; -.
DR CTD; 4862; -.
DR ZFIN; ZDB-GENE-030408-3; npas2.
DR eggNOG; KOG3561; Eukaryota.
DR HOGENOM; CLU_010044_2_2_1; -.
DR OMA; NQSHSAY; -.
DR OrthoDB; 2899615at2759; -.
DR TreeFam; TF324568; -.
DR Proteomes; UP000000437; Alternate scaffold 5.
DR Proteomes; UP000000437; Chromosome 5.
DR Bgee; ENSDARG00000016536; Expressed in retina and 17 other cell types or tissues.
DR GO; GO:1990513; C:CLOCK-BMAL transcription complex; IBA:GO_Central.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0032922; P:circadian regulation of gene expression; IBA:GO_Central.
DR GO; GO:0007623; P:circadian rhythm; IGI:ZFIN.
DR GO; GO:0009648; P:photoperiodism; IEP:ZFIN.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0009416; P:response to light stimulus; IGI:ZFIN.
DR CDD; cd19736; bHLH-PAS_PASD1; 1.
DR CDD; cd00130; PAS; 2.
DR Gene3D; 4.10.280.10; Helix-loop-helix DNA-binding domain; 1.
DR Gene3D; 3.30.450.20; PAS domain; 2.
DR InterPro; IPR011598; bHLH_dom.
DR InterPro; IPR047230; CLOCK-like.
DR InterPro; IPR036638; HLH_DNA-bd_sf.
DR InterPro; IPR001067; Nuc_translocat.
DR InterPro; IPR001610; PAC.
DR InterPro; IPR000014; PAS.
DR InterPro; IPR035965; PAS-like_dom_sf.
DR InterPro; IPR013767; PAS_fold.
DR PANTHER; PTHR46055:SF4; CIRCADIAN CLOCK PROTEIN PASD1; 1.
DR PANTHER; PTHR46055; CIRCADIAN LOCOMOTER OUTPUT CYCLES PROTEIN KAPUT; 1.
DR Pfam; PF00010; HLH; 1.
DR Pfam; PF00989; PAS; 1.
DR Pfam; PF14598; PAS_11; 1.
DR PRINTS; PR00785; NCTRNSLOCATR.
DR SMART; SM00353; HLH; 1.
DR SMART; SM00086; PAC; 1.
DR SMART; SM00091; PAS; 2.
DR SUPFAM; SSF47459; HLH, helix-loop-helix DNA-binding domain; 1.
DR SUPFAM; SSF55785; PYP-like sensor domain (PAS domain); 2.
DR PROSITE; PS50888; BHLH; 1.
DR PROSITE; PS50112; PAS; 2.
PE 2: Evidence at transcript level;
KW Activator {ECO:0000256|ARBA:ARBA00023159};
KW Biological rhythms {ECO:0000256|ARBA:ARBA00023108};
KW Coiled coil {ECO:0000256|SAM:Coils};
KW Reference proteome {ECO:0000313|Proteomes:UP000000437};
KW Repeat {ECO:0000256|ARBA:ARBA00022737}.
FT DOMAIN 42..94
FT /note="BHLH"
FT /evidence="ECO:0000259|PROSITE:PS50888"
FT DOMAIN 117..189
FT /note="PAS"
FT /evidence="ECO:0000259|PROSITE:PS50112"
FT DOMAIN 296..343
FT /note="PAS"
FT /evidence="ECO:0000259|PROSITE:PS50112"
FT REGION 1..54
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 435..487
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 494..513
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 579..628
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 808..845
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 535..569
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 25..54
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 808..839
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 845 AA; 95647 MW; 591A4443EB0F9946 CRC64;
MGEGVSMDNL SEFGGLCPSS RREWDTSSCV DDLMDEDEKD RAKRASRNKS EKKRRDQFNV
LIKELCTMLQ GQGHPRKMDK STILQRTIDF LQKQKEITAQ TESCEVRQDW KPSFLSNEEF
TQLMLEALDG FLIALTTDGN IIYVSDSVSS LIGHLPSDMV DQNILNFLPE REHADVYKLL
SSHMLLTESS TVDLLNSNET HVEFCCHIAR GNIDPKEPPT YEYVKFVGDF KFHNNVPLSS
CNGYDLAFPR TLQSSIEEQV CLVATVRLAT PQFLKDLCNV EDVCDEFTSR HSLEWKFLFL
DHRASPIIGY LPFEVLGTSG YDYYHVDDLE LIAQCHKQLM QCGKGKSCYY RFLTKGQQWI
WLQTHYYITY HQWNSKPEFI VCTHSVVSYA EVRAERRREF GLEESSSDMA TSSIKGQEVF
LDMCPPLEAT RDRINSARSV SSQSSRKSSH TALSDSASNS SVRYTEACTS SRQSASIGPE
KSSNRMTHTG TKTLIQRQSS SEPPSLSPSC SQHSAMTQSL YSFQQPQLGV MHQLKEQLEE
RTRILQADIK TQQQELHDIK EKLQLANLQM LLQQPIQGEF AGSGPQQQGP GRPAQQNTHP
KPQHCVSHSS HTLQPNSSST QGQQRLVQAG HMQAVSVPMQ THTSLTTPFY SNPMMFSPNH
GHRSQHDTHC QRNTHADYSQ DGQLRMLLNQ PMQTLVQDSN GGPQSSQCTS TIQQTKYPLE
QQMMAPSFPV QQVNCNAVLV PSPVFTSPIM IPHNSFITHQ TTPTYTTHPP VAPHSLPLQQ
PQQFFQMQPQ GLIHGTPTQA LFHTPSVPQQ STVGYVQPQQ QQQQQQHHHH SQSGNLSDYR
NMLPR
//
