PUF60_RAT
ID PUF60_RAT Reviewed; 564 AA.
AC Q9WV25;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 2.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Poly(U)-binding-splicing factor PUF60 {ECO:0000312|RGD:621674};
DE AltName: Full=60 kDa poly(U)-binding-splicing factor {ECO:0000312|RGD:621674};
DE AltName: Full=RNA-binding protein Siah-BP {ECO:0000250|UniProtKB:Q9UHX1};
DE AltName: Full=Siah-binding protein 1 {ECO:0000303|Ref.1};
GN Name=Puf60 {ECO:0000312|RGD:621674}; Synonyms=Siahbp1 {ECO:0000303|Ref.1};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RA Poleev A., Stamm S.;
RT "A sequence-specific RNA-binding protein homologous to human SiahBP.";
RL Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
CC -!- FUNCTION: DNA- and RNA-binding protein, involved in several nuclear
CC processes such as pre-mRNA splicing, apoptosis and transcription
CC regulation. In association with FUBP1 regulates MYC transcription at
CC the P2 promoter through the core-TFIIH basal transcription factor. Acts
CC as a transcriptional repressor through the core-TFIIH basal
CC transcription factor. Represses FUBP1-induced transcriptional
CC activation but not basal transcription. Decreases ERCC3 helicase
CC activity. Is also involved in pre-mRNA splicing. Promotes splicing of
CC an intron with weak 3'-splice site and pyrimidine tract in a
CC cooperative manner with U2AF2. Involved in apoptosis induction when
CC overexpressed in HeLa cells. Modulates alternative splicing of several
CC mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the
CC pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is
CC enhanced in presence of U2AF2. Binds to Y5 RNA in association with
CC RO60. Binds to poly(U) RNA (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Homodimer (By similarity). Associates with the spliceosome (By
CC similarity). Found in a complex with RO60 and Y5 RNA (By similarity).
CC Found in a complex with FUBP1 and far upstream element (FUSE) DNA
CC segment (By similarity). Interacts directly with ERCC3 (By similarity).
CC Interacts with CDK7 and GTF2H1 (By similarity). Interacts with
CC SRSF11/P54 (By similarity). {ECO:0000250|UniProtKB:Q9UHX1}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9UHX1}.
CC Note=Colocalizes partially with RO60. {ECO:0000250|UniProtKB:Q9UHX1}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9WV25-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9WV25-2; Sequence=VSP_027724;
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 -!- SIMILARITY: Belongs to the RRM half pint family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD44358.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AF165892; AAD44358.1; ALT_INIT; mRNA.
DR EMBL; AABR03055594; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_006241956.2; XM_006241894.3. [Q9WV25-1]
DR RefSeq; XP_006241957.2; XM_006241895.3. [Q9WV25-2]
DR AlphaFoldDB; Q9WV25; -.
DR BMRB; Q9WV25; -.
DR SMR; Q9WV25; -.
DR IntAct; Q9WV25; 3.
DR MINT; Q9WV25; -.
DR STRING; 10116.ENSRNOP00000053317; -.
DR iPTMnet; Q9WV25; -.
DR PhosphoSitePlus; Q9WV25; -.
DR jPOST; Q9WV25; -.
DR PaxDb; Q9WV25; -.
DR PRIDE; Q9WV25; -.
DR GeneID; 84401; -.
DR UCSC; RGD:621674; rat. [Q9WV25-1]
DR CTD; 22827; -.
DR RGD; 621674; Puf60.
DR VEuPathDB; HostDB:ENSRNOG00000009960; -.
DR eggNOG; KOG0124; Eukaryota.
DR HOGENOM; CLU_020551_3_1_1; -.
DR InParanoid; Q9WV25; -.
DR OrthoDB; 861359at2759; -.
DR PhylomeDB; Q9WV25; -.
DR TreeFam; TF313987; -.
DR Reactome; R-RNO-72163; mRNA Splicing - Major Pathway.
DR PRO; PR:Q9WV25; -.
DR Proteomes; UP000002494; Chromosome 7.
DR Bgee; ENSRNOG00000009960; Expressed in thymus and 19 other tissues.
DR ExpressionAtlas; Q9WV25; baseline and differential.
DR Genevisible; Q9WV25; RN.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; ISO:RGD.
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 Acetylation; Alternative splicing; Apoptosis; DNA-binding; Isopeptide bond;
KW mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Repressor; Ribonucleoprotein; RNA-binding;
KW Transcription; Transcription regulation; Ubl conjugation.
FT CHAIN 1..564
FT /note="Poly(U)-binding-splicing factor PUF60"
FT /id="PRO_0000299522"
FT DOMAIN 134..212
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 231..309
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 467..554
FT /note="RRM 3; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..521
FT /note="Inhibits homodimerization"
FT /evidence="ECO:0000250"
FT REGION 37..61
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 82..564
FT /note="Inhibits transcriptional repression, interaction
FT with ERCC3 and apoptosis induction"
FT /evidence="ECO:0000250"
FT REGION 421..442
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 46..61
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 421..441
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 65
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT MOD_RES 117
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT MOD_RES 249
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q3UEB3"
FT MOD_RES 256
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT MOD_RES 319
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT MOD_RES 459
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT CROSSLNK 48
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT CROSSLNK 85
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT CROSSLNK 424
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT CROSSLNK 463
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9UHX1"
FT VAR_SEQ 105..121
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_027724"
SQ SEQUENCE 564 AA; 60249 MW; C30B70E645AB0161 CRC64;
MATATIALQV NGQQGGGSEP AAAAAAAAAA VVAAGDKWKP PQGTESIKME NGQSTGTKLG
LPPLTPEQQE ALQKAKKYAM EQSIKSVLVK QTIAHQQQQL TNLQMAAVTM GFGDPLSPLQ
SMAAQRQRAL AIMCRVYVGS IYYELGEDTI RQAFAPFGPI KSIDMSWDSV TMKHKGFAFV
EYEVPEAAQL ALEQMNSVML GGRNIKVGRP SNIGQAQPII DQLAEEARAF NRIYVASVHQ
DLSDDDIKSV FEAFGKIKSC TLARDPTTGK HKGYGFIEYE KAQSSQDAVS SMNLFDLGGQ
YLRVGKAVTP PMPLLTPATP GGLPPAAAVA AAAATAKITA QEAVAGAAVL GTLATPGLVS
PALTLAQPLG ALPQAVMAAQ APGVITGVTP ARPPIPVTIP SVGVVNPILA SPPTLGLLEP
KKEKEEEELF PESERPEMLS EQEHMSISGS SARHMVMQKL LRKQESTVMV LRNMVDPKDI
DDDLEGEVTE ECGKFGAVNR VIIYQEKQGE EEDAEIIVKI FVEFSMASET HKAIQALNGR
WFGGRKVVAE VYDQERFDNS DLSA
