Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RNA-dependent RNA polymerase 6

Gene

RDR6

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

RNA-dependent RNA polymerase involved in post-transcriptional gene silencing (PTGS). Possesses ssRNA and ssDNA-dependent polymerase activity, but does not have priming activity. Possesses in vitro 3' nucleotidyltransferase activity in the presence of UTP as single nucleotide. Required for the production of 21 nucleotide trans-acting small interfering RNAs (ta-siRNAs) derived from TAS1, TAS2 and TAS3 endogenous transcripts. Acts in the RDR6/SGS3/DCL4/AGO7 ta-siRNA pathway involved in leaf developmental timing. Required for the production of natural siRNAs (nat-siRNAs) derived from cis-natural antisense transcripts. Required for the production of 24 nucleotide nat-siRNAs derived from the stress-related P5CDH-SRO5 antisense gene pair. Required for PTGS induced by transgene direct repeats. Plays an essential role in transitive silencing of transgenes by processing secondary siRNAs. This pathway, which requires DCL2 and DCL4, amplifies silencing by using the target RNA as substrate to generate secondary siRNAs, providing an efficient mechanism for long-distance silencing. Involved in the biogenesis of secondary siRNAs which require 22 nucleotide miRNAs associated to AGO1. Participates synergistically with AS1 and AS2 to proper plant development by repressing the miR165 and miR166 microRNAs (independently of AGO10) that may lead to mRNA degradation of genes in the class III HD-ZIP family. Required for the production of some small RNAs derived from the crucifer-infecting tobamovirus (TMV-cg). Required for sense virus-induced post-transcriptional gene silencing (S-PTGS).13 Publications

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

GO - Molecular functioni

  • DNA-directed DNA polymerase activity Source: UniProtKB-KW
  • RNA binding Source: UniProtKB-KW
  • RNA-directed 5'-3' RNA polymerase activity Source: TAIR

GO - Biological processi

  • carpel development Source: TAIR
  • defense response to virus Source: TAIR
  • gene silencing by RNA Source: TAIR
  • gynoecium development Source: TAIR
  • leaf development Source: TAIR
  • production of siRNA involved in RNA interference Source: TAIR
  • production of ta-siRNAs involved in RNA interference Source: TAIR
  • recognition of pollen Source: TAIR
  • RNA interference Source: TAIR
  • virus induced gene silencing Source: TAIR

Keywordsi

Molecular functionDNA-directed DNA polymerase, Nucleotidyltransferase, RNA-binding, RNA-directed RNA polymerase, Transferase
Biological processPlant defense, RNA-mediated gene silencing

Enzyme and pathway databases

BRENDAi2.7.7.48. 399.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-dependent RNA polymerase 6 (EC:2.7.7.48)
Short name:
AtRDRP6
Alternative name(s):
Protein SILENCING DEFECTIVE 1
Protein SUPPRESSOR OF GENE SILENCING 2
RNA-directed RNA polymerase 6
Gene namesi
Name:RDR6
Synonyms:RDRP6, SDE1, SGS2
Ordered Locus Names:At3g49500
ORF Names:T1G12.20, T9C5.95
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

AraportiAT3G49500.
TAIRilocus:2114633. AT3G49500.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: TAIR

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

First leaves are elongated and curl downward. Presence of stigmatic tissue in the middle of the septum at the apical end of the carpels. Altered post-transcriptional gene silencing (PTGS). Accumulation of ARF4 mRNA (targeted by TAS3-derived siRNAs). Upon infection, over-accumulation of CMV RNA and enhanced susceptibility to cucumber mosaic virus (CMV). Reduced levels of TMV-cg-derived small RNAs.6 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi429E → K: Alters post-transcriptional gene silencing. 1 Publication1
Mutagenesisi453E → K: Alters post-transcriptional gene silencing. 1 Publication1
Mutagenesisi611P → L: Alters post-transcriptional gene silencing. 1 Publication1
Mutagenesisi825G → E: Alters post-transcriptional gene silencing. 1 Publication1
Mutagenesisi826D → N: Alters post-transcriptional gene silencing. 2 Publications1
Mutagenesisi860S → F: Alters post-transcriptional gene silencing. 1 Publication1
Mutagenesisi866G → E in rdr6-13; alters post-transcriptional gene silencing. 2 Publications1
Mutagenesisi867D → A: Loss of polymerase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004046771 – 1196RNA-dependent RNA polymerase 6Add BLAST1196

Proteomic databases

PaxDbiQ9SG02.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

ExpressionAtlasiQ9SG02. baseline and differential.
GenevisibleiQ9SG02. AT.

Interactioni

Subunit structurei

Interacts with SGS3.1 Publication

Protein-protein interaction databases

BioGridi9430. 1 interactor.
IntActiQ9SG02. 1 interactor.
MINTiMINT-7014695.
STRINGi3702.AT3G49500.1.

Structurei

3D structure databases

ProteinModelPortaliQ9SG02.
SMRiQ9SG02.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RdRP family.Curated

Phylogenomic databases

eggNOGiKOG0988. Eukaryota.
ENOG410XQMQ. LUCA.
HOGENOMiHOG000239464.
InParanoidiQ9SG02.
KOiK11699.
OMAiHFARPEG.
OrthoDBiEOG093600H3.
PhylomeDBiQ9SG02.

Family and domain databases

InterProiView protein in InterPro
IPR007855. RNA-dep_RNA_pol_euk-typ.
IPR000504. RRM_dom.
PANTHERiPTHR23079. PTHR23079. 1 hit.
PfamiView protein in Pfam
PF05183. RdRP. 1 hit.
SUPFAMiSSF54928. SSF54928. 2 hits.

Sequencei

Sequence statusi: Complete.

Q9SG02-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGSEGNMKKS VVTQVSIGGF GESTTAKQLT DYLEDEVGIV WRCRLKTSWT
60 70 80 90 100
PPGSYPNFEI ADTSNIPSID EYKKVEPHAF VHFAVFESAG RAMDAAGQCN
110 120 130 140 150
LILDGQPLKV SLGPKNPYSL NQRRRTTVPY KLAGITLEIG TLVSRDDFFV
160 170 180 190 200
SWRAEGVDFL VDPFDNTCKF CFRKSTAFSF KDAVMHAVIN CDYKLELLVR
210 220 230 240 250
DIQTVRQYKT LHGFVLILQL ASSPRVWYRT ADDDIYDTVP GDLLDDDDPW
260 270 280 290 300
IRTTDFTQVG AIGRCHSYRV LISPRYENKL RTALDYFRMR RVQEERVRWP
310 320 330 340 350
PRIRNEPCFG EPVSDHFFCI HHKEGISFEI MFLVNSVLHR GVFNQFQLTE
360 370 380 390 400
RFFDLLRNQP KDVNIASLKH LCTYKRPVFD AYKRLKLVQE WIQKNPKLLG
410 420 430 440 450
SHEQSEDISE IRRLVITPTR AYCLPPEVEL SNRVLRRYKA VAERFLRVTF
460 470 480 490 500
MDESMQTINS NVLSYFVAPI VKDLTSSSFS QKTYVFKRVK SILTDGFKLC
510 520 530 540 550
GRKYSFLAFS ANQLRDRSAW FFAEDGKTRV SDIKTWMGKF KDKNVAKCAA
560 570 580 590 600
RMGLCFSSTY ATVDVMPHEV DTEVPDIERN GYVFSDGIGT ITPDLADEVM
610 620 630 640 650
EKLKLDVHYS PCAYQIRYAG FKGVVARWPS KSDGIRLALR DSMKKFFSKH
660 670 680 690 700
TILEICSWTR FQPGFLNRQI ITLLSVLGVP DEIFWDMQES MLYKLNRILD
710 720 730 740 750
DTDVAFEVLT ASCAEQGNTA AIMLSAGFKP KTEPHLRGML SSVRIAQLWG
760 770 780 790 800
LREKSRIFVT SGRWLMGCLD EAGILEHGQC FIQVSKPSIE NCFSKHGSRF
810 820 830 840 850
KETKTDLEVV KGYVAIAKNP CLHPGDVRIL EAVDVPQLHH MYDCLIFPQK
860 870 880 890 900
GDRPHTNEAS GSDLDGDLYF VAWDQKLIPP NRKSYPAMHY DAAEEKSLGR
910 920 930 940 950
AVNHQDIIDF FARNLANEQL GTICNAHVVH ADRSEYGAMD EECLLLAELA
960 970 980 990 1000
ATAVDFPKTG KIVSMPFHLK PKLYPDFMGK EDYQTYKSNK ILGRLYRRVK
1010 1020 1030 1040 1050
EVYDEDAEAS SEESTDPSAI PYDAVLEIPG FEDLIPEAWG HKCLYDGQLI
1060 1070 1080 1090 1100
GLLGQYKVQK EEEIVTGHIW SMPKYTSKKQ GELKERLKHS YNSLKKEFRK
1110 1120 1130 1140 1150
VFEETIPDHE NLSEEEKNIL YEKKASAWYH VTYHPEWVKK SLELQDPDES
1160 1170 1180 1190
SHAAMLSFAW IAADYLARIK IRSREMGSID SAKPVDSLAK FLAQRL
Length:1,196
Mass (Da):136,929
Last modified:May 1, 2000 - v1
Checksum:i812DEB9CEDC82C8F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti597D → G in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti646F → I in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti681D → V in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti696N → D in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti700D → V in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti805T → K in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti998R → P in AAF74208 (PubMed:10850496).Curated1
Sequence conflicti1044L → S in AAF74208 (PubMed:10850496).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF239718 Genomic DNA. Translation: AAF73959.1.
AF268093 Genomic DNA. Translation: AAF74208.1.
AC012329 Genomic DNA. Translation: AAG52184.1.
AL132964 Genomic DNA. Translation: CAB71285.1.
CP002686 Genomic DNA. Translation: AEE78550.1.
CP002686 Genomic DNA. Translation: ANM65667.1.
CP002686 Genomic DNA. Translation: ANM65668.1.
CP002686 Genomic DNA. Translation: ANM65669.1.
CP002686 Genomic DNA. Translation: ANM65670.1.
RefSeqiNP_001327617.1. NM_001339423.1.
NP_001327618.1. NM_001339424.1.
NP_001327619.1. NM_001339425.1.
NP_001327620.1. NM_001339426.1.
NP_190519.1. NM_114810.3.
UniGeneiAt.65263.

Genome annotation databases

EnsemblPlantsiAT3G49500.1; AT3G49500.1; AT3G49500.
AT3G49500.2; AT3G49500.2; AT3G49500.
AT3G49500.3; AT3G49500.3; AT3G49500.
AT3G49500.4; AT3G49500.4; AT3G49500.
AT3G49500.5; AT3G49500.5; AT3G49500.
GeneIDi824112.
GrameneiAT3G49500.1; AT3G49500.1; AT3G49500.
AT3G49500.2; AT3G49500.2; AT3G49500.
AT3G49500.3; AT3G49500.3; AT3G49500.
AT3G49500.4; AT3G49500.4; AT3G49500.
AT3G49500.5; AT3G49500.5; AT3G49500.
KEGGiath:AT3G49500.

Similar proteinsi

Entry informationi

Entry nameiRDR6_ARATH
AccessioniPrimary (citable) accession number: Q9SG02
Secondary accession number(s): A0A1I9LSW2, Q9LKP0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 8, 2011
Last sequence update: May 1, 2000
Last modified: July 5, 2017
This is version 109 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families