U2AFB_ORYSJ
ID U2AFB_ORYSJ Reviewed; 304 AA.
AC Q6AUG0; B7EHH7; Q9ZQW9;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2004, sequence version 1.
DT 25-MAY-2022, entry version 128.
DE RecName: Full=Splicing factor U2af small subunit B;
DE AltName: Full=U2 auxiliary factor 35 kDa subunit B;
DE AltName: Full=U2 small nuclear ribonucleoprotein auxiliary factor small subunit B;
DE Short=U2 snRNP auxiliary factor small subunit B;
DE AltName: Full=Zinc finger CCCH domain-containing protein 38;
DE Short=OsC3H38;
GN Name=U2AF35B; OrderedLocusNames=Os05g0564200, LOC_Os05g48960;
GN ORFNames=OsJ_018769, OsJ_19555 {ECO:0000312|EMBL:EEE64700.1},
GN OSJNBb0053D02.11;
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].
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=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
RN [3]
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 [4]
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 [5]
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 [6]
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 [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [8]
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 -!- SIMILARITY: Belongs to the splicing factor SR family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA77132.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
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DR EMBL; Y18348; CAA77132.1; ALT_SEQ; mRNA.
DR EMBL; AC124143; AAT77399.1; -; Genomic_DNA.
DR EMBL; AP008211; BAF18245.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS95352.1; -; Genomic_DNA.
DR EMBL; CM000142; EAZ35286.1; -; Genomic_DNA.
DR EMBL; CM000142; EEE64700.1; -; Genomic_DNA.
DR EMBL; AK070198; BAG91824.1; -; mRNA.
DR EMBL; AK104767; BAG96940.1; -; mRNA.
DR RefSeq; XP_015639721.1; XM_015784235.1.
DR RefSeq; XP_015639722.1; XM_015784236.1.
DR AlphaFoldDB; Q6AUG0; -.
DR SMR; Q6AUG0; -.
DR STRING; 4530.OS05T0564200-01; -.
DR PaxDb; Q6AUG0; -.
DR PRIDE; Q6AUG0; -.
DR EnsemblPlants; Os05t0564200-01; Os05t0564200-01; Os05g0564200.
DR GeneID; 4339621; -.
DR Gramene; Os05t0564200-01; Os05t0564200-01; Os05g0564200.
DR KEGG; osa:4339621; -.
DR eggNOG; KOG2202; Eukaryota.
DR HOGENOM; CLU_059852_2_1_1; -.
DR InParanoid; Q6AUG0; -.
DR OMA; RNPRHHE; -.
DR OrthoDB; 1340384at2759; -.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR Genevisible; Q6AUG0; 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; 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; 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 DNA-binding; Metal-binding; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Repeat; RNA-binding; Zinc; Zinc-finger.
FT CHAIN 1..304
FT /note="Splicing factor U2af small subunit B"
FT /id="PRO_0000346799"
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 184..304
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 184..203
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 204..223
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 257..304
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 304 AA; 34692 MW; E4CCA77054B79C02 CRC64;
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TVSPTIVLAN MYQRPDMITP
GVDAQGQPID PEKMQEHFED FYEDIYEELS KFGEVETLNV CDNLADHMIG NVYVQFREEE
QAVAAHNALQ GRFYSGRPII VEYSPVTDFR EATCRQFEEN SCNRGGYCNF MHVKQIGREL
RRKLYGGRSR RSHGRSRSPS PRHRRGNRDR DDFRRERDGY RGGGDGYRGG GGGGGGDGYR
GGDSYRGGGG GGRRGGGSRY DRYDDGGRRR HGSPPRRARS PVRESSEERR AKIEQWNRER
EEKP
