SYF2_HUMAN
ID SYF2_HUMAN Reviewed; 243 AA.
AC O95926; Q5TH73;
DT 19-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=Pre-mRNA-splicing factor SYF2;
DE AltName: Full=CCNDBP1-interactor;
DE AltName: Full=p29 {ECO:0000303|PubMed:11118353};
GN Name=SYF2; Synonyms=CBPIN, GCIPIP;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, AND INTERACTION WITH CCNDBP1.
RX PubMed=11118353; DOI=10.1006/bbrc.2000.3992;
RA Chang M.-S., Chang C.-L., Huang C.-J., Yang Y.-C.;
RT "p29, a novel GCIP-interacting protein, localizes in the nucleus.";
RL Biochem. Biophys. Res. Commun. 279:732-737(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain;
RX PubMed=11230166; DOI=10.1101/gr.gr1547r;
RA Wiemann S., Weil B., Wellenreuther R., Gassenhuber J., Glassl S.,
RA Ansorge W., Boecher M., Bloecker H., Bauersachs S., Blum H., Lauber J.,
RA Duesterhoeft A., Beyer A., Koehrer K., Strack N., Mewes H.-W.,
RA Ottenwaelder B., Obermaier B., Tampe J., Heubner D., Wambutt R., Korn B.,
RA Klein M., Poustka A.;
RT "Towards a catalog of human genes and proteins: sequencing and analysis of
RT 500 novel complete protein coding human cDNAs.";
RL Genome Res. 11:422-435(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Lung;
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 [5]
RP IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C
RP COMPLEX, FUNCTION, SUBCELLULAR LOCATION, AND SUBUNIT.
RX PubMed=11991638; DOI=10.1017/s1355838202021088;
RA Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.;
RT "Purification and characterization of native spliceosomes suitable for
RT three-dimensional structural analysis.";
RL RNA 8:426-439(2002).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [8]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-143 AND LYS-234, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [9] {ECO:0007744|PDB:5XJC}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.60 ANGSTROMS), FUNCTION, SUBUNIT, AND
RP SUBCELLULAR LOCATION.
RX PubMed=28502770; DOI=10.1016/j.cell.2017.04.033;
RA Zhang X., Yan C., Hang J., Finci L.I., Lei J., Shi Y.;
RT "An Atomic Structure of the Human Spliceosome.";
RL Cell 169:918-929(2017).
RN [10] {ECO:0007744|PDB:5MQF}
RP STRUCTURE BY ELECTRON MICROSCOPY (5.90 ANGSTROMS), FUNCTION, SUBUNIT,
RP SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=28076346; DOI=10.1038/nature21079;
RA Bertram K., Agafonov D.E., Liu W.T., Dybkov O., Will C.L., Hartmuth K.,
RA Urlaub H., Kastner B., Stark H., Luhrmann R.;
RT "Cryo-EM structure of a human spliceosome activated for step 2 of
RT splicing.";
RL Nature 542:318-323(2017).
CC -!- FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome
CC (PubMed:11991638, PubMed:28502770, PubMed:28076346).
CC {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770}.
CC -!- SUBUNIT: Identified in the spliceosome C complex (PubMed:11991638,
CC PubMed:28502770, PubMed:28076346). Interacts with CCNDBP1
CC (PubMed:11118353). {ECO:0000269|PubMed:11118353,
CC ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770}.
CC -!- INTERACTION:
CC O95926; Q9H6L4: ARMC7; NbExp=3; IntAct=EBI-2557644, EBI-742909;
CC O95926; O95273: CCNDBP1; NbExp=3; IntAct=EBI-2557644, EBI-748961;
CC O95926; P40692: MLH1; NbExp=3; IntAct=EBI-2557644, EBI-744248;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11118353,
CC ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O95926-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O95926-2; Sequence=VSP_054802;
CC -!- TISSUE SPECIFICITY: Abundantly expressed in the heart, skeletal muscle
CC and kidney. Expressed at lower level other tissues.
CC {ECO:0000269|PubMed:11118353}.
CC -!- SIMILARITY: Belongs to the SYF2 family. {ECO:0000305}.
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DR EMBL; AF273089; AAG42073.1; -; mRNA.
DR EMBL; AL080166; CAB45754.1; -; mRNA.
DR EMBL; AL031432; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC010862; AAH10862.1; -; mRNA.
DR CCDS; CCDS258.1; -. [O95926-2]
DR CCDS; CCDS259.1; -. [O95926-1]
DR PIR; T12485; T12485.
DR RefSeq; NP_056299.1; NM_015484.4. [O95926-1]
DR RefSeq; NP_997053.1; NM_207170.3. [O95926-2]
DR PDB; 5MQF; EM; 5.90 A; N=1-243.
DR PDB; 5XJC; EM; 3.60 A; M=1-243.
DR PDB; 5YZG; EM; 4.10 A; M=1-243.
DR PDB; 6ICZ; EM; 3.00 A; M=1-243.
DR PDB; 6ID0; EM; 2.90 A; M=1-243.
DR PDB; 6ID1; EM; 2.86 A; M=1-243.
DR PDB; 6QDV; EM; 3.30 A; y=100-239.
DR PDB; 7A5P; EM; 5.00 A; N=1-243.
DR PDBsum; 5MQF; -.
DR PDBsum; 5XJC; -.
DR PDBsum; 5YZG; -.
DR PDBsum; 6ICZ; -.
DR PDBsum; 6ID0; -.
DR PDBsum; 6ID1; -.
DR PDBsum; 6QDV; -.
DR PDBsum; 7A5P; -.
DR AlphaFoldDB; O95926; -.
DR SMR; O95926; -.
DR BioGRID; 117444; 71.
DR CORUM; O95926; -.
DR IntAct; O95926; 43.
DR MINT; O95926; -.
DR STRING; 9606.ENSP00000236273; -.
DR iPTMnet; O95926; -.
DR PhosphoSitePlus; O95926; -.
DR BioMuta; SYF2; -.
DR EPD; O95926; -.
DR jPOST; O95926; -.
DR MassIVE; O95926; -.
DR MaxQB; O95926; -.
DR PaxDb; O95926; -.
DR PeptideAtlas; O95926; -.
DR PRIDE; O95926; -.
DR ProteomicsDB; 51130; -. [O95926-1]
DR Antibodypedia; 34977; 214 antibodies from 32 providers.
DR DNASU; 25949; -.
DR Ensembl; ENST00000236273.9; ENSP00000236273.4; ENSG00000117614.10. [O95926-1]
DR Ensembl; ENST00000354361.3; ENSP00000346330.3; ENSG00000117614.10. [O95926-2]
DR GeneID; 25949; -.
DR KEGG; hsa:25949; -.
DR MANE-Select; ENST00000236273.9; ENSP00000236273.4; NM_015484.5; NP_056299.1.
DR UCSC; uc001bjt.2; human. [O95926-1]
DR CTD; 25949; -.
DR DisGeNET; 25949; -.
DR GeneCards; SYF2; -.
DR HGNC; HGNC:19824; SYF2.
DR HPA; ENSG00000117614; Low tissue specificity.
DR MIM; 607090; gene.
DR neXtProt; NX_O95926; -.
DR OpenTargets; ENSG00000117614; -.
DR PharmGKB; PA142670853; -.
DR VEuPathDB; HostDB:ENSG00000117614; -.
DR eggNOG; KOG2609; Eukaryota.
DR GeneTree; ENSGT00390000017845; -.
DR HOGENOM; CLU_051065_3_0_1; -.
DR InParanoid; O95926; -.
DR OMA; RRRMHND; -.
DR OrthoDB; 1565402at2759; -.
DR PhylomeDB; O95926; -.
DR TreeFam; TF313041; -.
DR PathwayCommons; O95926; -.
DR Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
DR SignaLink; O95926; -.
DR BioGRID-ORCS; 25949; 635 hits in 1083 CRISPR screens.
DR ChiTaRS; SYF2; human.
DR GenomeRNAi; 25949; -.
DR Pharos; O95926; Tbio.
DR PRO; PR:O95926; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; O95926; protein.
DR Bgee; ENSG00000117614; Expressed in calcaneal tendon and 206 other tissues.
DR Genevisible; O95926; HS.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IDA:UniProtKB.
DR GO; GO:0016607; C:nuclear speck; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IDA: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; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0048568; P:embryonic organ development; IEA:Ensembl.
DR GO; GO:0007369; P:gastrulation; IEA:Ensembl.
DR GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
DR GO; GO:0007095; P:mitotic G2 DNA damage checkpoint signaling; IEA:Ensembl.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IDA:UniProtKB.
DR GO; GO:0008284; P:positive regulation of cell population proliferation; IEA:Ensembl.
DR InterPro; IPR013260; mRNA_splic_SYF2.
DR PANTHER; PTHR13264; PTHR13264; 1.
DR Pfam; PF08231; SYF2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Coiled coil;
KW Isopeptide bond; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Spliceosome; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22814378"
FT CHAIN 2..243
FT /note="Pre-mRNA-splicing factor SYF2"
FT /id="PRO_0000250376"
FT COILED 66..91
FT /evidence="ECO:0000255"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:19413330,
FT ECO:0007744|PubMed:22814378"
FT CROSSLNK 143
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 234
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VAR_SEQ 45..86
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_054802"
FT VARIANT 89
FT /note="A -> V (in dbSNP:rs35324907)"
FT /id="VAR_062162"
FT HELIX 127..141
FT /evidence="ECO:0007829|PDB:6ID1"
FT HELIX 146..156
FT /evidence="ECO:0007829|PDB:6ID1"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:6ID1"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:6ICZ"
FT HELIX 176..194
FT /evidence="ECO:0007829|PDB:6ID1"
FT STRAND 211..213
FT /evidence="ECO:0007829|PDB:6ID1"
FT HELIX 214..225
FT /evidence="ECO:0007829|PDB:6ID1"
FT TURN 226..229
FT /evidence="ECO:0007829|PDB:6ID1"
FT HELIX 233..238
FT /evidence="ECO:0007829|PDB:6ID1"
SQ SEQUENCE 243 AA; 28722 MW; 6F910C13BC09A7F7 CRC64;
MAAIAASEVL VDSAEEGSLA AAAELAAQKR EQRLRKFREL HLMRNEARKL NHQEVVEEDK
RLKLPANWEA KKARLEWELK EEEKKKECAA RGEDYEKVKL LEISAEDAER WERKKKRKNP
DLGFSDYAAA QLRQYHRLTK QIKPDMETYE RLREKHGEEF FPTSNSLLHG THVPSTEEID
RMVIDLEKQI EKRDKYSRRR PYNDDADIDY INERNAKFNK KAERFYGKYT AEIKQNLERG
TAV
