SDN5_ARATH
ID SDN5_ARATH Reviewed; 567 AA.
AC Q8L7M4;
DT 25-NOV-2008, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 2.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Small RNA degrading nuclease 5;
DE EC=3.1.-.-;
GN Name=SDN5; OrderedLocusNames=At5g25800; ORFNames=F18A17.50;
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=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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 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 [4]
RP IDENTIFICATION.
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: Probable 3'-5' exonuclease degrading single-stranded small
CC RNAs.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8L7M4-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8L7M4-2; Sequence=VSP_035856, VSP_035857;
CC -!- SIMILARITY: Belongs to the REXO1/REXO3 family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC005405; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CP002688; AED93489.1; -; Genomic_DNA.
DR EMBL; AY128370; AAM91573.1; -; mRNA.
DR RefSeq; NP_197952.2; NM_122481.3. [Q8L7M4-1]
DR AlphaFoldDB; Q8L7M4; -.
DR SMR; Q8L7M4; -.
DR STRING; 3702.AT5G25800.1; -.
DR PaxDb; Q8L7M4; -.
DR PRIDE; Q8L7M4; -.
DR EnsemblPlants; AT5G25800.1; AT5G25800.1; AT5G25800. [Q8L7M4-1]
DR GeneID; 832649; -.
DR Gramene; AT5G25800.1; AT5G25800.1; AT5G25800. [Q8L7M4-1]
DR KEGG; ath:AT5G25800; -.
DR Araport; AT5G25800; -.
DR TAIR; locus:2145244; AT5G25800.
DR eggNOG; KOG2248; Eukaryota.
DR HOGENOM; CLU_008679_3_0_1; -.
DR InParanoid; Q8L7M4; -.
DR OMA; PDNAMLI; -.
DR PhylomeDB; Q8L7M4; -.
DR PRO; PR:Q8L7M4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8L7M4; baseline and differential.
DR Genevisible; Q8L7M4; 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..567
FT /note="Small RNA degrading nuclease 5"
FT /id="PRO_0000355088"
FT DOMAIN 215..364
FT /note="Exonuclease"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 8..22
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 282..298
FT /note="EEFLKLVFKETILVGHS -> YYTSIHMEDLIKLNFEF (in isoform
FT 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035856"
FT VAR_SEQ 299..567
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_035857"
FT CONFLICT 157
FT /note="P -> Q (in Ref. 3; AAM91573)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 567 AA; 62802 MW; 945D31CEB36FAACB CRC64;
MSSSKRKRGA ETAAEDCDDG TDKSNTGNSF FDIYGPEAKA ELDFKSPETT LNLQDVQGLV
TWVLAEGFMP SWVFIKNKPL IPKVVLLYLP GLDAALYLSH SKTLSSLKSC CGNPMALLAL
SCVVDEMRTI DTILTCKGRK KKTVTSSVEP PPLVSSPEAC NLMGKSFVEL TKDIPFPVSY
YTLSQKEMEQ NGYTFEKLEL TPTLPAPSGS CPPEIVALDC EMCITKEGLE LTRVTLVDIQ
GQVLLDKLVM PTNPITDYNT RYSGITAVMM EGVTTTLKDI QEEFLKLVFK ETILVGHSLE
NDLLSLKISH NLVIDTAVLY KHPHGRSYKT KLRILAKKFL AREIQESESG HDSAEDAKAA
MDLALLKIKH GPDFGSPPEV IRKKLLAVLN ESGKTTSIID NINIVKRYAS ESSNAIPVSS
DDEALSKAVK EVKNKRSQFV WTQFSELNAH FQSRADDPQK LNSRLAEMIS LLTCNKKSGL
KKSNVSPETK EILKKMNERV QSLYAALPTN AMFIVCTGHG DTSIVHRVRK MLKDEDEIGF
DREKLVKVLE ELQAQAEVAL CFVGIKQ
