SYF1_MOUSE
ID SYF1_MOUSE Reviewed; 855 AA.
AC Q9DCD2; Q8VDT5; Q9CVD8;
DT 15-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=Pre-mRNA-splicing factor SYF1;
DE AltName: Full=XPA-binding protein 2;
GN Name=Xab2; Synonyms=Syf1;
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 {ECO:0000312|EMBL:BAB22435.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Kidney, and Stomach;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [3]
RP DISRUPTION PHENOTYPE.
RX PubMed=15725628; DOI=10.1016/j.dnarep.2004.12.004;
RA Yonemasu R., Minami M., Nakatsu Y., Takeuchi M., Kuraoka I., Matsuda Y.,
RA Higashi Y., Kondoh H., Tanaka K.;
RT "Disruption of mouse XAB2 gene involved in pre-mRNA splicing, transcription
RT and transcription-coupled DNA repair results in preimplantation
RT lethality.";
RL DNA Repair 4:479-491(2005).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Spleen;
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: Involved in pre-mRNA splicing as component of the
CC spliceosome. Involved in transcription-coupled repair (TCR),
CC transcription and pre-mRNA splicing. {ECO:0000250|UniProtKB:Q9HCS7}.
CC -!- SUBUNIT: Associates with RNA polymerase II, the TCR-specific proteins
CC CKN1/CSA and ERCC6/CSB, and XPA. Identified in the spliceosome C
CC complex. Component of the XAB2 complex, a multimeric protein complex
CC composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE. Identified in a
CC pentameric intron-binding (IB) complex composed of AQR, XAB2, ISY1,
CC ZNF830 and PPIE that is incorporated into the spliceosome as a
CC preassembled complex. The IB complex does not contain PRPF19.
CC {ECO:0000250|UniProtKB:Q9HCS7}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q99PK0}.
CC Note=Detected in the splicing complex carrying pre-mRNA.
CC {ECO:0000250|UniProtKB:Q99PK0}.
CC -!- DISRUPTION PHENOTYPE: Complete embryonic lethality before 13.5 dpc.
CC Already at 3.5 dpc, the number of homozygous mutant embryos is lower
CC than expected. {ECO:0000269|PubMed:15725628}.
CC -!- SIMILARITY: Belongs to the crooked-neck family. {ECO:0000305}.
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DR EMBL; AK002890; BAB22435.1; -; mRNA.
DR EMBL; AK008628; BAB25790.1; -; mRNA.
DR EMBL; BC021341; AAH21341.1; -; mRNA.
DR CCDS; CCDS22065.1; -.
DR RefSeq; NP_080432.1; NM_026156.2.
DR AlphaFoldDB; Q9DCD2; -.
DR SMR; Q9DCD2; -.
DR BioGRID; 212186; 3.
DR IntAct; Q9DCD2; 1.
DR STRING; 10090.ENSMUSP00000019614; -.
DR iPTMnet; Q9DCD2; -.
DR PhosphoSitePlus; Q9DCD2; -.
DR EPD; Q9DCD2; -.
DR MaxQB; Q9DCD2; -.
DR PaxDb; Q9DCD2; -.
DR PRIDE; Q9DCD2; -.
DR ProteomicsDB; 258788; -.
DR Antibodypedia; 12104; 304 antibodies from 35 providers.
DR DNASU; 67439; -.
DR Ensembl; ENSMUST00000019614; ENSMUSP00000019614; ENSMUSG00000019470.
DR GeneID; 67439; -.
DR KEGG; mmu:67439; -.
DR UCSC; uc009kry.1; mouse.
DR CTD; 56949; -.
DR MGI; MGI:1914689; Xab2.
DR VEuPathDB; HostDB:ENSMUSG00000019470; -.
DR eggNOG; KOG2047; Eukaryota.
DR GeneTree; ENSGT00550000075140; -.
DR HOGENOM; CLU_007736_2_1_1; -.
DR InParanoid; Q9DCD2; -.
DR OMA; FLMQQPL; -.
DR OrthoDB; 370051at2759; -.
DR PhylomeDB; Q9DCD2; -.
DR TreeFam; TF300866; -.
DR Reactome; R-MMU-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-MMU-6782135; Dual incision in TC-NER.
DR Reactome; R-MMU-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-MMU-72163; mRNA Splicing - Major Pathway.
DR BioGRID-ORCS; 67439; 25 hits in 104 CRISPR screens.
DR ChiTaRS; Xab2; mouse.
DR PRO; PR:Q9DCD2; -.
DR Proteomes; UP000000589; Chromosome 8.
DR RNAct; Q9DCD2; protein.
DR Bgee; ENSMUSG00000019470; Expressed in floor plate of midbrain and 263 other tissues.
DR ExpressionAtlas; Q9DCD2; baseline and differential.
DR Genevisible; Q9DCD2; MM.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; ISO:MGI.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0071014; C:post-mRNA release spliceosomal complex; IBA:GO_Central.
DR GO; GO:0000974; C:Prp19 complex; IBA:GO_Central.
DR GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; ISS:UniProtKB.
DR GO; GO:0001824; P:blastocyst development; IMP:MGI.
DR GO; GO:0021987; P:cerebral cortex development; IEA:Ensembl.
DR GO; GO:0000349; P:generation of catalytic spliceosome for first transesterification step; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:0006351; P:transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; ISS:UniProtKB.
DR Gene3D; 1.25.40.10; -; 5.
DR InterPro; IPR003107; HAT.
DR InterPro; IPR045075; Syf1-like.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR InterPro; IPR019734; TPR_repeat.
DR PANTHER; PTHR11246; PTHR11246; 1.
DR Pfam; PF13181; TPR_8; 2.
DR SMART; SM00386; HAT; 10.
DR SMART; SM00028; TPR; 3.
DR SUPFAM; SSF48452; SSF48452; 4.
PE 1: Evidence at protein level;
KW Acetylation; DNA damage; DNA repair; mRNA processing; mRNA splicing;
KW Nucleus; Phosphoprotein; Reference proteome; Repeat; Spliceosome;
KW Transcription.
FT CHAIN 1..855
FT /note="Pre-mRNA-splicing factor SYF1"
FT /id="PRO_0000106415"
FT REPEAT 15..47
FT /note="HAT 1"
FT /evidence="ECO:0000305"
FT REPEAT 48..80
FT /note="HAT 2"
FT /evidence="ECO:0000305"
FT REPEAT 90..122
FT /note="HAT 3"
FT /evidence="ECO:0000305"
FT REPEAT 124..158
FT /note="HAT 4"
FT /evidence="ECO:0000305"
FT REPEAT 160..192
FT /note="HAT 5"
FT /evidence="ECO:0000305"
FT REPEAT 198..230
FT /note="HAT 6"
FT REPEAT 235..268
FT /note="HAT 7"
FT REPEAT 270..305
FT /note="HAT 8"
FT REPEAT 369..407
FT /note="HAT 9"
FT REPEAT 498..530
FT /note="HAT 10"
FT REPEAT 532..566
FT /note="HAT 11"
FT REPEAT 571..605
FT /note="HAT 12"
FT REPEAT 643..677
FT /note="HAT 13"
FT REPEAT 679..713
FT /note="HAT 14"
FT REGION 808..855
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 819..834
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 420
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9HCS7"
FT MOD_RES 851
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9HCS7"
FT CONFLICT 684
FT /note="A -> T (in Ref. 2; AAH21341)"
FT /evidence="ECO:0000305"
FT CONFLICT 842
FT /note="Q -> L (in Ref. 1; BAB25790)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 855 AA; 99988 MW; 6A5DA6A74E7FCB1D CRC64;
MVVMARVPRS ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK PRLNQLYERA
LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE RAFVFMHKMP RLWLDYCQFL
MDQGRVTHTR RTFDRALRAL PITQHSRIWP LYLRFLRSHP LPETAVRGYR RFLKLSPESA
EEYIEYLKSS DRLDEAAQRL ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV
DAIIRGGLTR FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA
QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL RQNPHHVHEW
HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA FAKFYEDNGQ LDDARVILEK
ATKVNFKQVD DLASVWCQCG ELELRHENYD EALKLLRKAT ALPARRAEYF DGSEPVQNRV
YKSLKVWSML ADLEESLGTF QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA
YERGISLFKW PNVSDIWSTY LTKFISRYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA
QLEEEWGLAR HAMAVYDRAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG IYQKAIEVLS
DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT GAFWQTWKDF EVRHGNEDTI
REMLRIRRSV QATYNTQVNF MASQMLKVSG SATGTVSDLA PGQSGMDDMK LLEQRAEQLA
AEAERDQPPR AQSKIFFVRS DASREELAEL AQQANPEEIQ LGEDEDEDEM DLEPNEVRLE
QQSVPAAVFG SLKED
