SMD1A_ARATH
ID SMD1A_ARATH Reviewed; 114 AA.
AC Q9SSF1; A0A1I9LP96; C0Z3G9;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Small nuclear ribonucleoprotein SmD1a {ECO:0000303|PubMed:15575968};
DE Short=AtSmD1-a {ECO:0000303|PubMed:15575968};
GN Name=SMD1A {ECO:0000303|PubMed:15575968};
GN OrderedLocusNames=At3g07590 {ECO:0000312|Araport:AT3G07590};
GN ORFNames=MLP3.4 {ECO:0000312|EMBL:AAF13077.1};
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf {ECO:0000312|EMBL:BAH57248.1};
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=15575968; DOI=10.1186/gb-2004-5-12-r102;
RA Wang B.B., Brendel V.;
RT "The ASRG database: identification and survey of Arabidopsis thaliana genes
RT involved in pre-mRNA splicing.";
RL Genome Biol. 5:R102.1-R102.23(2004).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND SUBCELLULAR LOCATION.
RX PubMed=26842463; DOI=10.1105/tpc.15.01045;
RA Elvira-Matelot E., Bardou F., Ariel F., Jauvion V., Bouteiller N.,
RA Le Masson I., Cao J., Crespi M.D., Vaucheret H.;
RT "The nuclear ribonucleoprotein SmD1 interplays with splicing, RNA quality
RT control, and posttranscriptional gene silencing in Arabidopsis.";
RL Plant Cell 28:426-438(2016).
CC -!- FUNCTION: Involved in splicing regulation. Facilitates post-
CC transcriptional gene silencing (PTGS) by limiting the degradation of
CC transgene aberrant RNAs by the RNA quality control (RQC) machinery,
CC thus favoring their entry into cytoplasmic siRNA bodies where they can
CC trigger PTGS. Does not participate in the production of small RNAs.
CC {ECO:0000269|PubMed:26842463}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:26842463}. Nucleus
CC speckle {ECO:0000250|UniProtKB:Q9SY09}. Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q9SY09}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q9SSF1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SSF1-2; Sequence=VSP_058954;
CC Name=3;
CC IsoId=Q9SSF1-3; Sequence=VSP_058953;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype (PubMed:26842463). Smd1a and
CC smd2b double mutants are embryo lethal (PubMed:26842463).
CC {ECO:0000269|PubMed:26842463}.
CC -!- MISCELLANEOUS: SMD1A and SMD1B have redundant activity, but consistent
CC with their expression level, SMD1B is more important than SMD1A and
CC either one copy of SMD1B or two copies of SMD1A is necessary for the
CC plant to survive. {ECO:0000305|PubMed:26842463}.
CC -!- SIMILARITY: Belongs to the snRNP core protein family. {ECO:0000305}.
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DR EMBL; AC009176; AAF13077.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74570.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE74571.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64404.1; -; Genomic_DNA.
DR EMBL; AY069907; AAL47458.1; -; mRNA.
DR EMBL; AY124838; AAM70547.1; -; mRNA.
DR EMBL; AK319133; BAH57248.1; -; mRNA.
DR EMBL; AY087568; AAM65110.1; -; mRNA.
DR RefSeq; NP_001189837.1; NM_001202908.2. [Q9SSF1-1]
DR RefSeq; NP_001326434.1; NM_001337723.1. [Q9SSF1-2]
DR RefSeq; NP_187416.1; NM_111638.5. [Q9SSF1-1]
DR AlphaFoldDB; Q9SSF1; -.
DR SMR; Q9SSF1; -.
DR STRING; 3702.AT3G07590.2; -.
DR PaxDb; Q9SSF1; -.
DR PRIDE; Q9SSF1; -.
DR ProteomicsDB; 234471; -. [Q9SSF1-1]
DR EnsemblPlants; AT3G07590.1; AT3G07590.1; AT3G07590. [Q9SSF1-1]
DR EnsemblPlants; AT3G07590.2; AT3G07590.2; AT3G07590. [Q9SSF1-1]
DR EnsemblPlants; AT3G07590.3; AT3G07590.3; AT3G07590. [Q9SSF1-2]
DR GeneID; 819950; -.
DR Gramene; AT3G07590.1; AT3G07590.1; AT3G07590. [Q9SSF1-1]
DR Gramene; AT3G07590.2; AT3G07590.2; AT3G07590. [Q9SSF1-1]
DR Gramene; AT3G07590.3; AT3G07590.3; AT3G07590. [Q9SSF1-2]
DR KEGG; ath:AT3G07590; -.
DR Araport; AT3G07590; -.
DR TAIR; locus:2091102; AT3G07590.
DR eggNOG; KOG3428; Eukaryota.
DR HOGENOM; CLU_123956_3_0_1; -.
DR InParanoid; Q9SSF1; -.
DR OMA; PTMNITL; -.
DR OrthoDB; 1579192at2759; -.
DR PhylomeDB; Q9SSF1; -.
DR PRO; PR:Q9SSF1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9SSF1; baseline and differential.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0000243; C:commitment complex; IBA:GO_Central.
DR GO; GO:0016607; C:nuclear speck; IDA:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0034715; C:pICln-Sm protein complex; IBA:GO_Central.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
DR GO; GO:0034719; C:SMN-Sm protein complex; IBA:GO_Central.
DR GO; GO:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0005685; C:U1 snRNP; IBA:GO_Central.
DR GO; GO:0005689; C:U12-type spliceosomal complex; IBA:GO_Central.
DR GO; GO:0005686; C:U2 snRNP; IBA:GO_Central.
DR GO; GO:0005687; C:U4 snRNP; IBA:GO_Central.
DR GO; GO:0005682; C:U5 snRNP; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0035194; P:post-transcriptional gene silencing by RNA; IMP:UniProtKB.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
DR CDD; cd01724; Sm_D1; 1.
DR InterPro; IPR027141; LSm4/Sm_D1/D3.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR InterPro; IPR034102; Sm_D1.
DR PANTHER; PTHR23338; PTHR23338; 1.
DR Pfam; PF01423; LSM; 1.
DR SMART; SM00651; Sm; 1.
DR SUPFAM; SSF50182; SSF50182; 1.
PE 3: Inferred from homology;
KW Alternative splicing; mRNA processing; Nucleus; Reference proteome; Repeat;
KW Ribonucleoprotein.
FT CHAIN 1..114
FT /note="Small nuclear ribonucleoprotein SmD1a"
FT /id="PRO_0000440135"
FT REPEAT 99..100
FT /note="1"
FT /evidence="ECO:0000305"
FT REPEAT 101..102
FT /note="2"
FT /evidence="ECO:0000305"
FT REPEAT 103..104
FT /note="3"
FT /evidence="ECO:0000305"
FT REPEAT 105..106
FT /note="4"
FT /evidence="ECO:0000305"
FT REPEAT 107..108
FT /note="5"
FT /evidence="ECO:0000305"
FT REPEAT 109..110
FT /note="6"
FT /evidence="ECO:0000305"
FT REPEAT 111..112
FT /note="7"
FT /evidence="ECO:0000305"
FT REPEAT 113..114
FT /note="8"
FT /evidence="ECO:0000305"
FT REGION 87..114
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 99..114
FT /note="8 X 2 AA tandem repeats of G-R"
FT /evidence="ECO:0000305"
FT COMPBIAS 93..114
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1..35
FT /note="Missing (in isoform 3)"
FT /id="VSP_058953"
FT VAR_SEQ 1..30
FT /note="MKLVRFLMKLNNETVSIELKNGTVVHGTIT -> MIWA (in isoform
FT 2)"
FT /id="VSP_058954"
SQ SEQUENCE 114 AA; 12600 MW; F2471793A626BA0A CRC64;
MKLVRFLMKL NNETVSIELK NGTVVHGTIT GVDVSMNTHL KTVKMSLKGK NPVTLDHLSL
RGNNIRYYIL PDSLNLETLL VEDTPRVKPK KPVAGKAVGR GRGRGRGRGR GRGR
