U2AFA_ORYSJ
ID U2AFA_ORYSJ Reviewed; 290 AA.
AC Q9ZQW8; A3C064; B7E7L8; Q9ZQW7;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 25-MAY-2022, entry version 125.
DE RecName: Full=Splicing factor U2af small subunit A;
DE AltName: Full=U2 auxiliary factor 35 kDa subunit A;
DE AltName: Full=U2 small nuclear ribonucleoprotein auxiliary factor small subunit A;
DE Short=U2 snRNP auxiliary factor small subunit A;
DE AltName: Full=Zinc finger CCCH domain-containing protein 60;
DE Short=OsC3H60;
GN Name=U2AF35A; OrderedLocusNames=Os09g0491756, LOC_Os09g31482;
GN ORFNames=OsJ_028686;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
RX PubMed=9852132; DOI=10.1074/jbc.273.51.34603;
RA Domon C., Lorkovic Z.J., Valcarcel J., Filipowicz W.;
RT "Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor
RT U2AF subunits expressed in higher plants.";
RL J. Biol. Chem. 273:34603-34610(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP NOMENCLATURE.
RX PubMed=18221561; DOI=10.1186/1471-2164-9-44;
RA Wang D., Guo Y., Wu C., Yang G., Li Y., Zheng C.;
RT "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.";
RL BMC Genomics 9:44-44(2008).
CC -!- FUNCTION: Necessary for the splicing of pre-mRNA. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9ZQW8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9ZQW8-2; Sequence=VSP_035015;
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DR EMBL; Y18349; CAA77133.1; -; mRNA.
DR EMBL; Y18349; CAA77134.1; -; mRNA.
DR EMBL; AC108762; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP008215; BAH94645.1; -; Genomic_DNA.
DR EMBL; AP014965; BAT08747.1; -; Genomic_DNA.
DR EMBL; CM000146; EAZ45203.1; -; Genomic_DNA.
DR EMBL; AK062560; BAG88365.1; -; mRNA.
DR EMBL; AK099481; BAG94151.1; -; mRNA.
DR RefSeq; XP_015611784.1; XM_015756298.1. [Q9ZQW8-1]
DR RefSeq; XP_015611785.1; XM_015756299.1. [Q9ZQW8-1]
DR AlphaFoldDB; Q9ZQW8; -.
DR SMR; Q9ZQW8; -.
DR STRING; 4530.OS09T0491756-01; -.
DR PaxDb; Q9ZQW8; -.
DR PRIDE; Q9ZQW8; -.
DR EnsemblPlants; Os09t0491756-01; Os09t0491756-01; Os09g0491756. [Q9ZQW8-1]
DR EnsemblPlants; Os09t0491756-02; Os09t0491756-02; Os09g0491756. [Q9ZQW8-1]
DR GeneID; 9268567; -.
DR Gramene; Os09t0491756-01; Os09t0491756-01; Os09g0491756. [Q9ZQW8-1]
DR Gramene; Os09t0491756-02; Os09t0491756-02; Os09g0491756. [Q9ZQW8-1]
DR KEGG; osa:9268567; -.
DR eggNOG; KOG2202; Eukaryota.
DR HOGENOM; CLU_059852_2_1_1; -.
DR InParanoid; Q9ZQW8; -.
DR OMA; FEEHSCN; -.
DR OrthoDB; 1340384at2759; -.
DR Proteomes; UP000000763; Chromosome 9.
DR Proteomes; UP000007752; Chromosome 9.
DR Proteomes; UP000059680; Chromosome 9.
DR Genevisible; Q9ZQW8; OS.
DR GO; GO:0005681; C:spliceosomal complex; IBA:GO_Central.
DR GO; GO:0089701; C:U2AF complex; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030628; F:pre-mRNA 3'-splice site binding; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR003954; RRM_dom_euk.
DR InterPro; IPR009145; U2AF_small.
DR InterPro; IPR000571; Znf_CCCH.
DR PANTHER; PTHR12620; PTHR12620; 1.
DR Pfam; PF00076; RRM_1; 1.
DR Pfam; PF00642; zf-CCCH; 2.
DR PRINTS; PR01848; U2AUXFACTOR.
DR SMART; SM00360; RRM; 1.
DR SMART; SM00361; RRM_1; 1.
DR SMART; SM00356; ZnF_C3H1; 2.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 1.
DR PROSITE; PS50103; ZF_C3H1; 2.
PE 2: Evidence at transcript level;
KW Alternative splicing; DNA-binding; Metal-binding; mRNA processing;
KW mRNA splicing; Nucleus; Reference proteome; Repeat; RNA-binding; Zinc;
KW Zinc-finger.
FT CHAIN 1..290
FT /note="Splicing factor U2af small subunit A"
FT /id="PRO_0000346798"
FT DOMAIN 44..146
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT ZN_FING 12..40
FT /note="C3H1-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 148..175
FT /note="C3H1-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT REGION 188..290
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 188..203
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 204..258
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 265..290
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 256..271
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:9852132"
FT /id="VSP_035015"
SQ SEQUENCE 290 AA; 34088 MW; 8A2DA713C55D261A CRC64;
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNKP SVSPTLLLSN MYLRPDMITP
GIDAQGNPID PEKIQADFED FYEDIFEELS KYGEIESLHV CDNFADHMIG NVYVQFREED
QAARALQALT GRYYSGRPII VEFSPVSDFR EATCRQYEEN SCNRGGYCNF MHVKEIGRDL
RKRLFGHLHR SRRSHSHGRS RSPSPYHYRR DYDRRSSSRS RDHDDYYRGG SHDYYRGGSR
RSSERHRSSY DSDGSRRRHR SRTRSPVRDG SEERRAQIEQ WNREREAAQV
