SMD1B_ARATH
ID SMD1B_ARATH Reviewed; 116 AA.
AC Q9SY09; F4JHV8;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 25-MAY-2022, entry version 155.
DE RecName: Full=Small nuclear ribonucleoprotein SmD1b {ECO:0000303|PubMed:15575968};
DE Short=AtSmD1-b {ECO:0000303|PubMed:15575968};
GN Name=SMD1B {ECO:0000303|PubMed:15575968};
GN OrderedLocusNames=At4g02840 {ECO:0000312|Araport:AT4G02840};
GN ORFNames=T5J8.16 {ECO:0000312|EMBL:AAD15345.1};
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=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 [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=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Bautista V.R., Kim C.J., Chen H., Quinitio C., Ecker J.R.;
RT "Arabidopsis ORF Clones.";
RL Submitted (SEP-2006) 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 speckle {ECO:0000269|PubMed:26842463}.
CC Nucleus, nucleolus {ECO:0000269|PubMed:26842463}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9SY09-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SY09-2; Sequence=VSP_058955;
CC -!- DISRUPTION PHENOTYPE: Post-transcriptional gene silencing deficiency
CC and developmental defects, including reduced stature, leaf serration
CC and early flowering (PubMed:26842463). Smd1a and smd2b double mutants
CC are embryo lethal (PubMed:26842463). {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; AC004044; AAD15345.1; -; Genomic_DNA.
DR EMBL; AL161495; CAB77769.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE82236.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE82237.1; -; Genomic_DNA.
DR EMBL; AK117672; BAC42325.1; -; mRNA.
DR EMBL; BT028879; ABI49426.1; -; mRNA.
DR EMBL; AY084707; AAM61281.1; -; mRNA.
DR PIR; B85036; B85036.
DR RefSeq; NP_001190664.1; NM_001203735.1. [Q9SY09-2]
DR RefSeq; NP_192193.1; NM_116518.4. [Q9SY09-1]
DR AlphaFoldDB; Q9SY09; -.
DR SMR; Q9SY09; -.
DR IntAct; Q9SY09; 3.
DR STRING; 3702.AT4G02840.2; -.
DR PRIDE; Q9SY09; -.
DR ProteomicsDB; 234530; -. [Q9SY09-1]
DR EnsemblPlants; AT4G02840.1; AT4G02840.1; AT4G02840. [Q9SY09-1]
DR EnsemblPlants; AT4G02840.2; AT4G02840.2; AT4G02840. [Q9SY09-2]
DR GeneID; 828163; -.
DR Gramene; AT4G02840.1; AT4G02840.1; AT4G02840. [Q9SY09-1]
DR Gramene; AT4G02840.2; AT4G02840.2; AT4G02840. [Q9SY09-2]
DR KEGG; ath:AT4G02840; -.
DR Araport; AT4G02840; -.
DR TAIR; locus:2140240; AT4G02840.
DR eggNOG; KOG3428; Eukaryota.
DR HOGENOM; CLU_123956_3_0_1; -.
DR OMA; SVTPQMN; -.
DR OrthoDB; 1579192at2759; -.
DR PhylomeDB; Q9SY09; -.
DR PRO; PR:Q9SY09; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9SY09; 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: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:0003729; F:mRNA binding; IDA:UniProtKB.
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:0043484; P:regulation of RNA splicing; IMP:UniProtKB.
DR GO; GO:0008380; P:RNA splicing; IMP:TAIR.
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; Nucleus; Reference proteome; Repeat;
KW Ribonucleoprotein.
FT CHAIN 1..116
FT /note="Small nuclear ribonucleoprotein SmD1b"
FT /id="PRO_0000440136"
FT REPEAT 100..101
FT /note="1"
FT /evidence="ECO:0000305"
FT REPEAT 102..103
FT /note="2"
FT /evidence="ECO:0000305"
FT REPEAT 104..105
FT /note="3"
FT /evidence="ECO:0000305"
FT REPEAT 106..107
FT /note="4"
FT /evidence="ECO:0000305"
FT REPEAT 108..109
FT /note="5"
FT /evidence="ECO:0000305"
FT REPEAT 110..111
FT /note="6"
FT /evidence="ECO:0000305"
FT REPEAT 112..113
FT /note="7"
FT /evidence="ECO:0000305"
FT REPEAT 114..116
FT /note="8; approximate"
FT /evidence="ECO:0000305"
FT REGION 85..116
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 100..116
FT /note="8 X 2 AA approximate tandem repeats of G-R"
FT /evidence="ECO:0000305"
FT COMPBIAS 102..116
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 30
FT /note="T -> TDEYTRFYLNR (in isoform 2)"
FT /id="VSP_058955"
SQ SEQUENCE 116 AA; 12750 MW; 4ABA07CBD18F2152 CRC64;
MKLVRFLMKL NNETVSIELK NGTIVHGTIT GVDVSMNTHL KAVKLTLKGK NPVTLDHLSV
RGNNIRYYIL PDSLNLETLL VEDTPRIKPK KPTAGKIPAG RGRGRGRGRG RGRGGR
