ID   PU60B_DANRE             Reviewed;         516 AA.
AC   Q6IQE0; Q7ZZ33; Q7ZZ34;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   13-NOV-2007, sequence version 2.
DT   03-AUG-2022, entry version 129.
DE   RecName: Full=Poly(U)-binding-splicing factor PUF60-B;
GN   Name=puf60b; Synonyms=puf60; ORFNames=si:zc12p8.2, zgc:86806;
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 [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   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC   TISSUE=Embryo;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=24140112; DOI=10.1016/j.ajhg.2013.09.010;
RA   Dauber A., Golzio C., Guenot C., Jodelka F.M., Kibaek M., Kjaergaard S.,
RA   Leheup B., Martinet D., Nowaczyk M.J., Rosenfeld J.A., Zeesman S.,
RA   Zunich J., Beckmann J.S., Hirschhorn J.N., Hastings M.L., Jacquemont S.,
RA   Katsanis N.;
RT   "SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the
RT   8q24.3 copy-number variant.";
RL   Am. J. Hum. Genet. 93:798-811(2013).
CC   -!- FUNCTION: DNA- and RNA-binding protein, involved in transcription
CC       repression and pre-mRNA splicing. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1;
CC         IsoId=Q6IQE0-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q6IQE0-2; Sequence=VSP_029175;
CC       Name=3;
CC         IsoId=Q6IQE0-3; Sequence=VSP_029175, VSP_029176;
CC   -!- DOMAIN: The third RNA recognition motif, called PUMP domain, is
CC       atypical and may rather mediate homodimerization and/or protein-protein
CC       interactions.
CC   -!- DISRUPTION PHENOTYPE: Morpholino-mediated knockdown of the gene results
CC       in embryos with reduced body length, microcephaly, retrognathia and
CC       heart edema. {ECO:0000269|PubMed:24140112}.
CC   -!- SIMILARITY: Belongs to the RRM half pint family. {ECO:0000305}.
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DR   EMBL; AL772146; CAD61098.1; -; Genomic_DNA.
DR   EMBL; AL772146; CAD61099.1; -; Genomic_DNA.
DR   EMBL; BC071467; AAH71467.1; -; mRNA.
DR   RefSeq; NP_001002121.1; NM_001002121.1. [Q6IQE0-3]
DR   AlphaFoldDB; Q6IQE0; -.
DR   SMR; Q6IQE0; -.
DR   STRING; 7955.ENSDARP00000034301; -.
DR   PaxDb; Q6IQE0; -.
DR   PRIDE; Q6IQE0; -.
DR   Ensembl; ENSDART00000166448; ENSDARP00000141568; ENSDARG00000001241. [Q6IQE0-3]
DR   GeneID; 415211; -.
DR   KEGG; dre:415211; -.
DR   CTD; 415211; -.
DR   ZFIN; ZDB-GENE-040625-116; puf60b.
DR   eggNOG; KOG0124; Eukaryota.
DR   GeneTree; ENSGT00940000155594; -.
DR   HOGENOM; CLU_020551_3_1_1; -.
DR   InParanoid; Q6IQE0; -.
DR   OrthoDB; 861359at2759; -.
DR   PhylomeDB; Q6IQE0; -.
DR   TreeFam; TF313987; -.
DR   PRO; PR:Q6IQE0; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 7.
DR   Bgee; ENSDARG00000001241; Expressed in gastrula and 29 other tissues.
DR   ExpressionAtlas; Q6IQE0; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0000380; P:alternative mRNA splicing, via spliceosome; IBA:GO_Central.
DR   GO; GO:0006915; P:apoptotic process; IEA:UniProtKB-KW.
DR   GO; GO:0006376; P:mRNA splice site selection; IBA:GO_Central.
DR   GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; IBA:GO_Central.
DR   CDD; cd12370; RRM1_PUF60; 1.
DR   CDD; cd12371; RRM2_PUF60; 1.
DR   CDD; cd12648; RRM3_UHM_PUF60; 1.
DR   Gene3D; 3.30.70.330; -; 3.
DR   InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR   InterPro; IPR006532; PUF60-like.
DR   InterPro; IPR034209; PUF60_RRM1.
DR   InterPro; IPR034211; PUF60_RRM2.
DR   InterPro; IPR034212; PUF60_RRM3.
DR   InterPro; IPR035979; RBD_domain_sf.
DR   InterPro; IPR000504; RRM_dom.
DR   InterPro; IPR003954; RRM_dom_euk.
DR   Pfam; PF00076; RRM_1; 2.
DR   SMART; SM00360; RRM; 3.
DR   SMART; SM00361; RRM_1; 2.
DR   SUPFAM; SSF54928; SSF54928; 2.
DR   TIGRFAMs; TIGR01645; half-pint; 1.
DR   PROSITE; PS50102; RRM; 3.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Apoptosis; DNA-binding; mRNA processing;
KW   mRNA splicing; Nucleus; Reference proteome; Repeat; Repressor;
KW   Ribonucleoprotein; RNA-binding; Transcription; Transcription regulation.
FT   CHAIN           1..516
FT                   /note="Poly(U)-binding-splicing factor PUF60-B"
FT                   /id="PRO_0000299523"
FT   DOMAIN          86..164
FT                   /note="RRM 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT   DOMAIN          183..261
FT                   /note="RRM 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT   DOMAIN          419..506
FT                   /note="RRM 3; atypical"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT   REGION          356..398
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        371..386
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   VAR_SEQ         57..73
FT                   /note="Missing (in isoform 2 and isoform 3)"
FT                   /evidence="ECO:0000303|Ref.2"
FT                   /id="VSP_029175"
FT   VAR_SEQ         333..342
FT                   /note="LSTTKTVFHL -> VTPARPTLPVVPQ (in isoform 3)"
FT                   /evidence="ECO:0000303|Ref.2"
FT                   /id="VSP_029176"
SQ   SEQUENCE   516 AA;  55420 MW;  105C2A4CD905D976 CRC64;
     MENGQGTGSK LGLPPLTPEQ QEALQKAKKY AMEQSIKSVL VKQTIAHQQQ QLTNLQMAAV
     TMGFGDPLSS LQSVAAQRQR ALAIMCRVYV GSIYYELGED TIRQAFAPFG PIKSIDMSWD
     SVTMKHKGFA FVEYEVPEAA QLALEQMNSV MLGGRNIKVG RPGSIGQAQP IIEQLAEEAR
     AYNRIYVASI HPDLSDDDIK SVFEAFGKIK SCMLAREPTT GKHKGFGFIE YEKPQSSLDA
     VSSMNLFDLG GQYLRVGKAV TPPMPLLTPT TPGGLPPAAA VAAAAATAKI TAQEAVAGTV
     LSSLASPAHI LSQQMGLPQA VLAAQAPGII TGLSTTKTVF HLVGLVNPVL ASPPVTAPAS
     MGTPTSAVQL HTEVKREEDS RRTAEDHSAP VGNGQDSELE RLSVSASAGR QAAIQSKSTV
     MVLRNMVGPE DIDDDLEGEV MEECGKYGAV NRVIIYQERQ GEEDDAEIIV KIFVEFSDAG
     EMNKAIQALN NRWFAGRKVV AELYDQDRFN SSDLTA