SCAF4_RAT
ID SCAF4_RAT Reviewed; 1200 AA.
AC Q63627; F1LSM7;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 03-JUL-2019, sequence version 2.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=SR-related and CTD-associated factor 4 {ECO:0000305};
DE AltName: Full=CTD-binding SR-like protein RA4 {ECO:0000305};
DE AltName: Full=Splicing factor, arginine/serine-rich 15 {ECO:0000305};
GN Name=Scaf4 {ECO:0000312|RGD:727896};
GN Synonyms=Sfrs15 {ECO:0000312|RGD:727896};
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 [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).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 153-1200, AND INTERACTION WITH POLR2A.
RC TISSUE=Hippocampus;
RX PubMed=8692929; DOI=10.1073/pnas.93.14.6975;
RA Yuryev A., Patturajan M., Litingtung Y., Joshi R.V., Gentile C., Gebara M.,
RA Corden J.L.;
RT "The C-terminal domain of the largest subunit of RNA polymerase II
RT interacts with a novel set of serine/arginine-rich proteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:6975-6980(1996).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1178, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Anti-terminator protein required to prevent early mRNA
CC termination during transcription. Together with SCAF8, acts by
CC suppressing the use of early, alternative poly(A) sites, thereby
CC preventing the accumulation of non-functional truncated proteins.
CC Mechanistically, associates with the phosphorylated C-terminal
CC heptapeptide repeat domain (CTD) of the largest RNA polymerase II
CC subunit (POLR2A), and subsequently binds nascent RNA upstream of early
CC polyadenylation sites to prevent premature mRNA transcript cleavage and
CC polyadenylation. Independently of SCAF8, also acts as a suppressor of
CC transcriptional readthrough. {ECO:0000250|UniProtKB:O95104}.
CC -!- SUBUNIT: Interacts with POLR2A; via C-terminal heptapeptide repeat
CC domain (CTD) phosphorylated at 'Ser-2' and 'Ser-5'.
CC {ECO:0000269|PubMed:8692929}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O95104}.
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DR EMBL; AABR07033613; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U49058; AAC52660.1; -; mRNA.
DR PIR; T31425; T31425.
DR AlphaFoldDB; Q63627; -.
DR SMR; Q63627; -.
DR STRING; 10116.ENSRNOP00000047258; -.
DR iPTMnet; Q63627; -.
DR jPOST; Q63627; -.
DR PaxDb; Q63627; -.
DR PeptideAtlas; Q63627; -.
DR PRIDE; Q63627; -.
DR UCSC; RGD:727896; rat.
DR RGD; 727896; Scaf4.
DR VEuPathDB; HostDB:ENSRNOG00000002104; -.
DR eggNOG; KOG0132; Eukaryota.
DR HOGENOM; CLU_005263_0_1_1; -.
DR InParanoid; Q63627; -.
DR OMA; AEGDKNH; -.
DR PhylomeDB; Q63627; -.
DR TreeFam; TF324527; -.
DR PRO; PR:Q63627; -.
DR Proteomes; UP000002494; Chromosome 11.
DR Bgee; ENSRNOG00000002104; Expressed in testis and 19 other tissues.
DR ExpressionAtlas; Q63627; baseline and differential.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0008022; F:protein C-terminus binding; IPI:RGD.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IMP:RGD.
DR GO; GO:2000805; P:negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled; ISS:UniProtKB.
DR CDD; cd12461; RRM_SCAF4; 1.
DR Gene3D; 1.25.40.90; -; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR006569; CID_dom.
DR InterPro; IPR008942; ENTH_VHS.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR034369; SCAF4_RRM.
DR Pfam; PF04818; CID; 1.
DR Pfam; PF00076; RRM_1; 1.
DR SMART; SM00582; RPR; 1.
DR SMART; SM00360; RRM; 1.
DR SUPFAM; SSF48464; SSF48464; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS51391; CID; 1.
DR PROSITE; PS50102; RRM; 1.
PE 1: Evidence at protein level;
KW Acetylation; Nucleus; Phosphoprotein; Reference proteome; RNA-binding;
KW Transcription; Transcription regulation.
FT CHAIN 1..1200
FT /note="SR-related and CTD-associated factor 4"
FT /id="PRO_0000081944"
FT DOMAIN 1..139
FT /note="CID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00724"
FT DOMAIN 574..648
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 140..172
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 299..324
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 346..566
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 696..724
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 834..875
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 927..1200
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 142..157
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 365..465
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 501..543
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 544..562
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 927..962
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 983..1044
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1045..1142
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1150..1164
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 49
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:O95104"
FT MOD_RES 154
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95104"
FT MOD_RES 722
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95104"
FT MOD_RES 1058
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95104"
FT MOD_RES 1178
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT CONFLICT 189
FT /note="A -> D (in Ref. 2; AAC52660)"
FT CONFLICT 425
FT /note="P -> A (in Ref. 2; AAC52660)"
FT CONFLICT 430
FT /note="P -> A (in Ref. 2; AAC52660)"
FT CONFLICT 792..793
FT /note="LR -> WG (in Ref. 2; AAC52660)"
FT CONFLICT 897
FT /note="A -> G (in Ref. 2; AAC52660)"
SQ SEQUENCE 1200 AA; 130953 MW; 7593A48AEED1B4F5 CRC64;
MDAVNAFNQE LFSLMDMKPP ISRAKMILIT KAAIKAIKLY KHVVQIVEKF IKKCKPEYKV
PGLYVIDSIV RQSRHQFGTD KDVFGPRFSK NITATFQYLY LCPSEDKSKI VRVLNLWQKN
GVFKIEIIQP LLDMAAGTSN AAPGAENVTN NEGSPPPPVK VSSELPQAPT NSMPAVPQLP
SSDAFAAVAQ LFQTTQGQQL QQILQTFQQP PKPQSPALDS AVMAQVQAIT AQLKTAPTQP
PEQKTAFDKK LLDRFDYDDE PEAVEDSKKE DAVAVATTAL ATAAPPVPAA ATPAVAPAVP
ASSATSPPPP QAPFGYPGDG MQQPAYTQHQ NVDQFQPRMM ALQQDSMQHQ VPLPPNGQMP
GFGLLSAPPP FPPMPQPGMP QPGMPQPGMP QPGLSQPGLP QPGMPQPGMP QPGMPQPGMP
QPGLPQPGLP QPGMPQPGMP QPGMPQPGMP QPGMPPTPPV QPTFQPTFQP QNEPHSQKPH
QQEMEVEQPC VTEVKRHVPE SRKSRSRSPK RRRSRSGSRS RRSRHRRSRS RSRDRRRHSP
RSRSQERRDR EKERERRQKG LPQIKSETAS VCSTTLWVGQ LDKRTTQQDV ASLLEEFGPI
ESINMIPPRG CAYIVMVHRQ DAYRALQKLS RGNYKVNQKS IKIAWALNKG IKADFKQYWD
VELGVTYIPW DKVKAEELES FCEGGMLDSD TLNPDWKGIP KKPENEVAQN GGAEASHTEP
VSPIPKPVPV PVPALPVPAP ITVPPPQVPP HQPGPPVVGA LQPPAFTPPL GIPPPGFGPG
VPPPPPPPPP FLRPGFNPMH LPPGFLPPGP PPPITPPVSI PPPHTPPISI PNLVSGARGN
AESADSAKMY GSAGPPAAPT SLPTPPVTQP VSLLGTQGVA PGPVIGLQAP STGLLGARPG
LIPLQRPPGM PPPHLQRFPM MPPRPMPPHM MHRGPPPGPG GFAMPPPHGM KGPFPPHGPF
VRPGGMPGLG GPGPGPGGSE DRDGRQQQPQ QQQQQQQQQQ QQQQQQQQQP PPQQSQTQQQ
PAPSQQPAPA QQQPQQFRND NRQQFNSGRD QERFGRRSFG SRVENDRERY GSRSDERDNS
NRERREWGRR SPERDRHRDL EERSRRSSGH RDRDRDSRDR ESRREKEESR GKEKHEVADR
AGGNKAVEAP LSQVGNTDTV SELNKGEAMA TVVKPEESPA EATSSVEPEK DSGSAAEAPR
