U2A2A_ARATH
ID U2A2A_ARATH Reviewed; 573 AA.
AC O23212; Q3E9P9; Q8RXR7;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 2.
DT 25-MAY-2022, entry version 151.
DE RecName: Full=Splicing factor U2af large subunit A {ECO:0000303|PubMed:24580679};
DE AltName: Full=U2 auxiliary factor 65 kDa subunit A {ECO:0000303|PubMed:24580679};
DE AltName: Full=U2 small nuclear ribonucleoprotein auxiliary factor large subunit A {ECO:0000303|PubMed:24580679};
DE Short=U2 snRNP auxiliary factor large subunit A {ECO:0000303|PubMed:24580679};
GN Name=U2AF65A {ECO:0000303|PubMed:24580679};
GN OrderedLocusNames=At4g36690 {ECO:0000312|Araport:AT4G36690};
GN ORFNames=C7A10.670 {ECO:0000312|EMBL:CAB16828.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 83-573 (ISOFORM 3).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [6]
RP INTERACTION WITH SUA.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=20525852; DOI=10.1105/tpc.110.074674;
RA Sugliani M., Brambilla V., Clerkx E.J., Koornneef M., Soppe W.J.;
RT "The conserved splicing factor SUA controls alternative splicing of the
RT developmental regulator ABI3 in Arabidopsis.";
RL Plant Cell 22:1936-1946(2010).
RN [7]
RP INTERACTION WITH SF1, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=24580679; DOI=10.1111/tpj.12491;
RA Jang Y.H., Park H.-Y., Lee K.C., Thu M.P., Kim S.-K., Suh M.C., Kang H.,
RA Kim J.-K.;
RT "A homolog of splicing factor SF1 is essential for development and is
RT involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana.";
RL Plant J. 78:591-603(2014).
CC -!- FUNCTION: Necessary for the splicing of pre-mRNA. {ECO:0000250}.
CC -!- SUBUNIT: Component of the spliceosome (Probable). Interacts with SUA
CC (PubMed:20525852). Interacts with SF1 in the nucleus (PubMed:24580679).
CC {ECO:0000269|PubMed:20525852, ECO:0000269|PubMed:24580679,
CC ECO:0000305}.
CC -!- INTERACTION:
CC O23212; F4JCU0: SUA; NbExp=3; IntAct=EBI-4439005, EBI-4427912;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:24580679}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=O23212-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O23212-2; Sequence=VSP_035548, VSP_035549;
CC Name=3;
CC IsoId=O23212-3; Sequence=VSP_035547, VSP_035550;
CC -!- DOMAIN: N-terminal RS domain has a very strong bias in favor of D over
CC S.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to intron retention.
CC {ECO:0000305}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the splicing factor SR family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BX827587; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=BX827587; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
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DR EMBL; Z99708; CAB16828.1; -; Genomic_DNA.
DR EMBL; AL161589; CAB80335.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86687.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86688.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE86689.1; -; Genomic_DNA.
DR EMBL; AF462805; AAL58899.1; -; mRNA.
DR EMBL; AY080711; AAL85029.1; -; mRNA.
DR EMBL; AY143980; AAN28919.1; -; mRNA.
DR EMBL; BT000965; AAN41365.1; -; mRNA.
DR EMBL; BX827587; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; C85433; C85433.
DR RefSeq; NP_195387.1; NM_119833.4. [O23212-1]
DR RefSeq; NP_849509.1; NM_179178.3. [O23212-2]
DR RefSeq; NP_974695.1; NM_202966.4. [O23212-3]
DR AlphaFoldDB; O23212; -.
DR SMR; O23212; -.
DR BioGRID; 15103; 15.
DR IntAct; O23212; 15.
DR STRING; 3702.AT4G36690.1; -.
DR iPTMnet; O23212; -.
DR PaxDb; O23212; -.
DR PRIDE; O23212; -.
DR ProteomicsDB; 228669; -. [O23212-1]
DR EnsemblPlants; AT4G36690.1; AT4G36690.1; AT4G36690. [O23212-1]
DR EnsemblPlants; AT4G36690.2; AT4G36690.2; AT4G36690. [O23212-2]
DR EnsemblPlants; AT4G36690.3; AT4G36690.3; AT4G36690. [O23212-3]
DR GeneID; 829822; -.
DR Gramene; AT4G36690.1; AT4G36690.1; AT4G36690. [O23212-1]
DR Gramene; AT4G36690.2; AT4G36690.2; AT4G36690. [O23212-2]
DR Gramene; AT4G36690.3; AT4G36690.3; AT4G36690. [O23212-3]
DR KEGG; ath:AT4G36690; -.
DR Araport; AT4G36690; -.
DR TAIR; locus:2115280; AT4G36690.
DR eggNOG; KOG0120; Eukaryota.
DR InParanoid; O23212; -.
DR PhylomeDB; O23212; -.
DR PRO; PR:O23212; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O23212; baseline and differential.
DR Genevisible; O23212; AT.
DR GO; GO:0000243; C:commitment complex; IBA:GO_Central.
DR GO; GO:0016607; C:nuclear speck; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0071004; C:U2-type prespliceosome; IBA:GO_Central.
DR GO; GO:0089701; C:U2AF complex; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0008187; F:poly-pyrimidine tract binding; IBA:GO_Central.
DR GO; GO:0030628; F:pre-mRNA 3'-splice site binding; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; ISS:TAIR.
DR Gene3D; 3.30.70.330; -; 3.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR006529; U2AF_lg.
DR Pfam; PF00076; RRM_1; 1.
DR SMART; SM00360; RRM; 2.
DR SUPFAM; SSF54928; SSF54928; 2.
DR TIGRFAMs; TIGR01642; U2AF_lg; 1.
DR PROSITE; PS50102; RRM; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Repeat; RNA-binding; Spliceosome.
FT CHAIN 1..573
FT /note="Splicing factor U2af large subunit A"
FT /id="PRO_0000352267"
FT DOMAIN 239..322
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 359..437
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 478..564
FT /note="RRM 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..175
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..95
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 105..140
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 506..565
FT /note="GALTNVVIPRPSPNGEPVAGLGKVFLKYADTDGSTRARFGMNGRKFGGNEVV
FT AVYYPEDK -> AFCYKESALTYTDRRLHKPPNLFITNGHYFLKEKTDLFLSVFSCLVF
FT EMFCSLTLKMQVL (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_035547"
FT VAR_SEQ 507..542
FT /note="ALTNVVIPRPSPNGEPVAGLGKVFLKYADTDGSTRA -> KRPLNCAIWSIL
FT KYKIKSILICLSVFLVVLFYSLLL (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035548"
FT VAR_SEQ 543..573
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035549"
FT VAR_SEQ 566..573
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_035550"
SQ SEQUENCE 573 AA; 63551 MW; 7253F15AF9B9092B CRC64;
MSEFEDHEGN GTVADAIYDE ENGGRDGEIE DQLDSKPKRE SRDHERETSR SKDREREKGR
DKDRERDSEV SRRSRDRDGE KSKERSRDKD RDHRERHHRS SRHRDHSRER GERRERGGRD
DDDYRRSRDR DHDRRRDDRG GRRSRRSRSR SKDRSERRTR SRSPSKSKQR VSGFDMAPPA
SAMLAAGAAV TGQVPPAPPT LPGAGMFPNM FPLPTGQSFG GLSMMPIQAM TQQATRHARR
VYVGGLSPTA NEQSVATFFS QVMAAVGGNT AGPGDAVVNV YINHEKKFAF VEMRSVEEAS
NAMSLDGIIF EGAPVKVRRP SDYNPSLAAT LGPSQPSPHL NLAAVGLTPG ASGGLEGPDR
IFVGGLPYYF TESQVRELLE SFGGLKGFDL VKDRETGNSK GYAFCVYQDL SVTDIACAAL
NGIKMGDKTL TVRRANQGTM LQKPEQENVL LHAQQQIAFQ RVMLQPGAVA TTVVCLTQVV
TEDELRDDEE YGDIMEDMRQ EGGKFGALTN VVIPRPSPNG EPVAGLGKVF LKYADTDGST
RARFGMNGRK FGGNEVVAVY YPEDKFEQGD YGA
