SCAF4_MOUSE
ID SCAF4_MOUSE Reviewed; 1183 AA.
AC Q7TSH6; A0A338P6Z6; Q69ZP8; Q6PFF0; Q8R1B3;
DT 03-JUL-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 132.
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|MGI:MGI:2146350};
GN Synonyms=Kiaa1172 {ECO:0000303|PubMed:15368895},
GN Srsf15 {ECO:0000312|MGI:MGI:2146350};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Fetal brain;
RX PubMed=15368895; DOI=10.1093/dnares/11.3.205;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
RA Saga Y., Seino S., Nishimura M., Kaisho T., Hoshino K., Kitamura H.,
RA Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: IV.
RT The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs
RT identified by screening of terminal sequences of cDNA clones randomly
RT sampled from size-fractionated libraries.";
RL DNA Res. 11:205-218(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3).
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19144319; DOI=10.1016/j.immuni.2008.11.006;
RA Trost M., English L., Lemieux S., Courcelles M., Desjardins M.,
RA Thibault P.;
RT "The phagosomal proteome in interferon-gamma-activated macrophages.";
RL Immunity 30:143-154(2009).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
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:0000250|UniProtKB:O95104}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O95104}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q7TSH6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q7TSH6-2; Sequence=VSP_060218;
CC Name=3;
CC IsoId=Q7TSH6-3; Sequence=VSP_060219, VSP_060220;
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH24860.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAD32398.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AK173120; BAD32398.1; ALT_INIT; mRNA.
DR EMBL; AC139573; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC024860; AAH24860.1; ALT_INIT; mRNA.
DR EMBL; BC053096; AAH53096.1; -; mRNA.
DR EMBL; BC057592; AAH57592.1; -; mRNA.
DR CCDS; CCDS37396.1; -. [Q7TSH6-3]
DR CCDS; CCDS84260.1; -. [Q7TSH6-1]
DR CCDS; CCDS88967.1; -. [Q7TSH6-2]
DR RefSeq; NP_001333728.1; NM_001346799.1. [Q7TSH6-1]
DR RefSeq; NP_849254.2; NM_178923.4. [Q7TSH6-3]
DR RefSeq; XP_006523075.1; XM_006523012.2.
DR AlphaFoldDB; Q7TSH6; -.
DR SMR; Q7TSH6; -.
DR STRING; 10090.ENSMUSP00000044472; -.
DR iPTMnet; Q7TSH6; -.
DR PhosphoSitePlus; Q7TSH6; -.
DR jPOST; Q7TSH6; -.
DR MaxQB; Q7TSH6; -.
DR PeptideAtlas; Q7TSH6; -.
DR PRIDE; Q7TSH6; -.
DR ProteomicsDB; 328722; -.
DR ProteomicsDB; 330275; -. [Q7TSH6-1]
DR Antibodypedia; 6761; 103 antibodies from 24 providers.
DR Ensembl; ENSMUST00000039280; ENSMUSP00000044472; ENSMUSG00000022983. [Q7TSH6-3]
DR Ensembl; ENSMUST00000163419; ENSMUSP00000132250; ENSMUSG00000022983. [Q7TSH6-1]
DR Ensembl; ENSMUST00000232371; ENSMUSP00000156174; ENSMUSG00000022983. [Q7TSH6-2]
DR GeneID; 224432; -.
DR KEGG; mmu:224432; -.
DR UCSC; uc007zwb.2; mouse.
DR UCSC; uc007zwd.2; mouse. [Q7TSH6-1]
DR CTD; 57466; -.
DR MGI; MGI:2146350; Scaf4.
DR VEuPathDB; HostDB:ENSMUSG00000022983; -.
DR eggNOG; KOG0132; Eukaryota.
DR GeneTree; ENSGT00530000063946; -.
DR HOGENOM; CLU_005263_0_1_1; -.
DR OMA; AEGDKNH; -.
DR OrthoDB; 821342at2759; -.
DR TreeFam; TF324527; -.
DR BioGRID-ORCS; 224432; 16 hits in 72 CRISPR screens.
DR ChiTaRS; Scaf4; mouse.
DR PRO; PR:Q7TSH6; -.
DR Proteomes; UP000000589; Chromosome 16.
DR Bgee; ENSMUSG00000022983; Expressed in dorsal pancreas and 276 other tissues.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0008022; F:protein C-terminus binding; ISO:MGI.
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; ISO:MGI.
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; Alternative splicing; Methylation; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding; Transcription; Transcription regulation.
FT CHAIN 1..1183
FT /note="SR-related and CTD-associated factor 4"
FT /id="PRO_0000447631"
FT DOMAIN 1..139
FT /note="CID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00724"
FT DOMAIN 569..643
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 299..324
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 348..561
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 691..722
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 800..859
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 920..1183
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 365..382
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 398..412
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 428..454
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 455..472
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 496..538
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 539..557
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 800..823
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 920..956
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 977..1003
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1029..1125
FT /note="Basic and acidic 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 717
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95104"
FT MOD_RES 1042
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:O95104"
FT VAR_SEQ 477
FT /note="Q -> QV (in isoform 2)"
FT /id="VSP_060218"
FT VAR_SEQ 501
FT /note="S -> SRSAS (in isoform 3)"
FT /id="VSP_060219"
FT VAR_SEQ 827
FT /note="L -> STIAGINEDTTKDLSIGNPIPTV (in isoform 3)"
FT /id="VSP_060220"
FT CONFLICT 326
FT /note="Y -> C (in Ref. 1; BAD32398)"
FT /evidence="ECO:0000305"
FT CONFLICT 954
FT /note="F -> L (in Ref. 3; AAH24860)"
FT /evidence="ECO:0000305"
FT CONFLICT 999
FT /note="Missing (in Ref. 1; BAD32398)"
FT /evidence="ECO:0000305"
FT CONFLICT 1165
FT /note="V -> A (in Ref. 1; BAD32398)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1183 AA; 129056 MW; 525A0CD9AEB7213B CRC64;
MDAVNAFNQE LFSLMDMKPP ISRAKMILIT KAAIKAIKLY KHVVQIVEKF IKKCKPEYKV
PGLYVIDSIV RQSRHQFGTD KDVFGPRFSK NITATFQYLY LCPSEDKSKI VRVLNLWQKN
GVFKIEIIQP LLDMAAGTSN AAPVAENVTN NEGSPPPPVK ISSELAQAPT NSMPTVAQLP
SSDAFAAVAQ LFQTTQGQQL QQILQTFQQP PQPQSPALDS AVMAQVQAIT AQLKTAPTQP
PEQKTAFDKK LLDRFDYDDE PEAVEDSKKE DAAAISTAAL ATAAPPAPTA ATPAVATAVP
VPSATSPPPP QTPFGYPGDG VQQPAYTQHQ SMDQFQPRMM PIQQDTMHHQ VPLPPNGQMP
GFGLLSAPPP FPPMPQPGMP QPGMAQPGLA QPGMAQPTMP QPGMPQPGMP QPGMAQPGLA
QPGMAQPGMP QPAMPQPAMP QPGMAQPGVS PAPPVQPTFQ STFQPQNEPH SQKPHQQEME
VEQPCVTEVK RHVPESRKSR SRSPKRRRSR SGSRSRRSRH RRSRSRSRDR RRHSPRSRSQ
ERRDREKERE RRQKGLPQIK SETASVCSTT LWVGQLDKRT TQQDVASLLE EFGPIESINM
IPPRGCAYIV MVHRQDAYRA LQKLSRGNYK VNQKSIKIAW ALNKGIKADY KQYWDVELGV
TYIPWDKVKA EELESFCEGG MLDSDTLNPD WKGIPKKPDN EVAQNGGAET SHTEPVSPIP
KPVPVPVPPI PVPAPITVPP PQVPPHQPGP PVVGALQPPA FTPPLGMPPP GFGPGVPPPP
PPPPFLRPGF NPMHLPPGFL PPGPPPPITP PVSIPPPHTP PISIPNLVSG ARGNAESGDS
AKMYGSAGPP AAPTSLPTPP VTQPVSLLGT QGVAPGPVIG LQAPSTGLLG ARPGLIPLQR
PPGMPPPHLQ RFPMMPPRPM PPHMMHRGPP PGPGGFAMPP PHGMKGPFPP HGPFVRPGGM
PGLGGPGPGP GASEDRDGRQ QQPQQQPPPQ QQQQQQQPQQ QPPQQSPSQQ PAPAQQQPPQ
FRNDSRQQFN SGRDQERFGR RSFGSRVEND RERYGSRNDD RDNSNRERRE WGRRSPDRDR
HRDLEERSRR SSGHRDRDRD SRDRESRREK EENRKEKHEV ADRAGGNKAV EPPLSQVGTI
DTVSELNKGE AMATVVKPEE SPAEVTSPVG PEKDPGSAAE PPR
