SDN2_ARATH
ID SDN2_ARATH Reviewed; 466 AA.
AC Q9FFG1; B3H5L2;
DT 25-NOV-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Small RNA degrading nuclease 2;
DE EC=3.1.-.-;
GN Name=SDN2; OrderedLocusNames=At5g05540; ORFNames=MOP10.8;
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=9330910; DOI=10.1093/dnares/4.3.215;
RA Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence
RT features of the 1.6 Mb regions covered by twenty physically assigned P1
RT clones.";
RL DNA Res. 4:215-230(1997).
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 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 [5]
RP IDENTIFICATION, AND DISRUPTION PHENOTYPE.
RX PubMed=18787168; DOI=10.1126/science.1163728;
RA Ramachandran V., Chen X.;
RT "Degradation of microRNAs by a family of exoribonucleases in Arabidopsis.";
RL Science 321:1490-1492(2008).
CC -!- FUNCTION: 3'-5' exonuclease degrading single-stranded small RNAs.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9FFG1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9FFG1-2; Sequence=VSP_035854, VSP_035855;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy with
CC other SDN ribonucleases. Simultaneous knockdown of SDN1, SDN2 and SDN3
CC results in elevated miRNA levels and pleiotropic developmental defects.
CC {ECO:0000269|PubMed:18787168}.
CC -!- SIMILARITY: Belongs to the REXO1/REXO3 family. {ECO:0000305}.
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DR EMBL; AB005241; BAB11543.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90885.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90886.1; -; Genomic_DNA.
DR EMBL; BT009685; AAP81803.1; -; mRNA.
DR EMBL; AK118437; BAC43046.1; -; mRNA.
DR RefSeq; NP_001119175.1; NM_001125703.2. [Q9FFG1-2]
DR RefSeq; NP_196173.1; NM_120636.4. [Q9FFG1-1]
DR AlphaFoldDB; Q9FFG1; -.
DR SMR; Q9FFG1; -.
DR IntAct; Q9FFG1; 1.
DR STRING; 3702.AT5G05540.1; -.
DR PaxDb; Q9FFG1; -.
DR PRIDE; Q9FFG1; -.
DR ProteomicsDB; 232667; -. [Q9FFG1-1]
DR EnsemblPlants; AT5G05540.1; AT5G05540.1; AT5G05540. [Q9FFG1-1]
DR EnsemblPlants; AT5G05540.2; AT5G05540.2; AT5G05540. [Q9FFG1-2]
DR GeneID; 830437; -.
DR Gramene; AT5G05540.1; AT5G05540.1; AT5G05540. [Q9FFG1-1]
DR Gramene; AT5G05540.2; AT5G05540.2; AT5G05540. [Q9FFG1-2]
DR KEGG; ath:AT5G05540; -.
DR Araport; AT5G05540; -.
DR TAIR; locus:2169717; AT5G05540.
DR eggNOG; KOG2248; Eukaryota.
DR InParanoid; Q9FFG1; -.
DR OMA; AICGKEV; -.
DR OrthoDB; 774159at2759; -.
DR PhylomeDB; Q9FFG1; -.
DR PRO; PR:Q9FFG1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FFG1; baseline and differential.
DR Genevisible; Q9FFG1; AT.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0004527; F:exonuclease activity; IBA:GO_Central.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR CDD; cd06145; REX1_like; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR013520; Exonuclease_RNaseT/DNA_pol3.
DR InterPro; IPR034922; REX1-like_exo.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF00929; RNase_T; 1.
DR SMART; SM00479; EXOIII; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Exonuclease; Hydrolase; Nuclease; Nucleus;
KW Reference proteome.
FT CHAIN 1..466
FT /note="Small RNA degrading nuclease 2"
FT /id="PRO_0000355085"
FT DOMAIN 142..298
FT /note="Exonuclease"
FT REGION 426..466
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 435..466
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 352
FT /note="P -> V (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_035854"
FT VAR_SEQ 353..466
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_035855"
SQ SEQUENCE 466 AA; 53182 MW; B8864C96239C6CE3 CRC64;
MEDVLATAEG VVLVKLVKVA QKLGLKGENG TWKEFLDFYD KQLGSSSLSD PSKRRKDDLV
AFLTTLKKKE DLQLLAKSLK LDNDVFEKFK KKSLDETAEQ RLVRMTLTHD EYPLDYLFPS
NAEDWVRTGL GKKKMEPTKI EMIAIDCEMV LCEDGSEAVV RVAAVDRDLK VILDEFVKPN
QPVVDYRTFI TGLTAQDLEK ATISVVDIQE KLLMFISEDT ILVGQSLNHD LKVLKVDHAR
VIDTSLVFKY NYDGTRRPLR LKRPSLNYLC KCILGYEVQK EGVPHNCVHD AEAAMKLVLA
ILDNGAETSV PLSKEMLEAE KSKLYLHRIP CNVPYEELNG VVSRDIPHEV KPSKKQDRHY
YSAIVVFKSP EEANQAFENI AGDFGKDSRG LSQKQIFLEP SSSEPRLYVL VRKMVEDDLV
GEVIAEENNA SSKKRKRENH SKGTRDRRRC KPLSRRKQRS NVKRRR
