GGRNA | Results

Matches are highlighted with green background. Overlapping matches are dark colored.

Arabidopsis thaliana RNA polymerase II, Rpb4, core protein (NRPD4), mRNA. (814 bp)

inference="similar to RNA sequence, EST:INSD:ES197708.1,INSD:EL316587.1,INSD:ES205252.1, INSD:ES196420.1" /exception="annotated by transcript or proteomic data" /note="NRPD4; FUNCTIONS IN: DNA-directed RNA polymerase activity, nucleotide binding, catalytic activity; INVOLVED IN: RNA interference, interphase, production of siRNA involved in RNA interference, DNA methylation on cytosine within a CHH sequence; LOCATED IN: DNA-directed RNA polymerase V complex, nucleus, DNA-directed RNA polymerase IV complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro...

Synonym: DL4012W; FCAALL.240; NRPE4; RDM2; RNA-DIRECTED DNA METHYLATION 2
NM_117687.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana Argonaute family protein (AGO7), mRNA. (3443 bp)

F10D13.11; F10D13_11; ZIP; ZIPPY" /inference="Similar to RNA sequence, EST:INSD:ES195631.1,INSD:ES164500.1,INSD:ES212862.1, INSD:Z34562.1,INSD:ES008820.1,INSD:Z34563.1" /note="ARGONAUTE7 (AGO7); FUNCTIONS IN: nucleic acid binding; INVOLVED IN: production of ta-siRNAs involved in RNA interference, vegetative phase change, production of lsiRNA involved in RNA interference, regulation of development, heterochronic, gene silencing by miRNA; LOCATED IN: cellular_component unknown; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: Domain of unknown...

Synonym: ARGONAUTE7; F10D13.11; F10D13_11; ZIP; ZIPPY
NM_105611.5 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana RNA helicase (LBA1), mRNA. (4547 bp)

Arabidopsis thaliana" /mol_type="mRNA" /db_xref="taxon:3702" /chromosome="5" /ecotype="Columbia" gene 1..4547 /gene="LBA1" /locus_tag="AT5G47010" /gene_synonym="ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1" /note="Required for nonsense-mediated mRNA decay. Involved in RNA interference. lba1 mutants has reduced sugar-induced expression of Atb- amylase, is hypersensitive to glucose and abscisic acid and resistant to mannose, and shows early flowering, short day-sensitive growth, and seed germination phenotypes." /db_xref="Araport:AT5G47010" /db_xref="GeneID:834747" /db_xref="TAIR:...

Synonym: ATUPF1; LOW-LEVEL BETA-AMYLASE 1; MQD22.15; MQD22_15; UPF1
NM_124072.3 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana histone deacetylase-related / HD-like protein (HDT4), mRNA. (792 bp)

INSD:BP671651.1, INSD:Z26451.1,INSD:AI999559.1,INSD:DR325152.1, INSD:ES111786.1,INSD:ES131334.1,INSD:EH909696.1" /inference="similar to RNA sequence, mRNA:INSD:BT008535.1,INSD:AF255713.1" /note="HDT4; FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: production of siRNA involved in RNA interference; LOCATED IN: nucleolus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: histone deacetylase 2B (TAIR:AT5G22650.2); Has 725 Blast hits to 661 proteins in 171 species: Archae - 0; Bacteria - 166; Metazoa - 184; Fungi - 55;...

Synonym: F15K20.6; F15K20_6; HD2D; HDA13; HDT04; HISTONE DEACETYLASE; HISTONE DEACETYLASE 13; histone deacetylase 2D
NM_179778.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana histone deacetylase-related / HD-like protein (HDT4), mRNA. (973 bp)

INSD:BP843415.1,INSD:AU239128.1,INSD:DR325151.1, INSD:ES111786.1,INSD:ES131334.1,INSD:EH909696.1" /inference="similar to RNA sequence, mRNA:INSD:AK229619.1,INSD:BX821834.1,INSD:BT006162.1" /note="HDT4; FUNCTIONS IN: histone deacetylase activity; INVOLVED IN: production of siRNA involved in RNA interference; LOCATED IN: nucleolus; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: histone deacetylase 3 (TAIR:AT3G44750.2); Has 818 Blast hits to 747 proteins in 183 species: Archae - 0; Bacteria - 171; Metazoa - 199; Fungi - 55;...

Synonym: F15K20.6; F15K20_6; HD2D; HDA13; HDT04; HISTONE DEACETYLASE; HISTONE DEACETYLASE 13; histone deacetylase 2D
NM_001336129.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana silencing defective 5 (SDE5), mRNA. (1227 bp)

Araport:AT3G15390" /db_xref="GeneID:820778" /db_xref="TAIR:AT3G15390" CDS 161..1060 /gene="SDE5" /locus_tag="AT3G15390" /gene_synonym="silencing defective 5" /note="silencing defective 5 (SDE5); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: production of ta-siRNAs involved in RNA interference; LOCATED IN: cellular_component unknown; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 12 growth stages; CONTAINS InterPro DOMAIN/s: Domain of unknown function DUF1771 (InterPro:IPR013899); BEST Arabidopsis thaliana protein match is: smr (Small MutS Related) domain-containing protein...

Synonym: silencing defective 5
NM_001202971.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana uncharacterized protein (AT3G17712), mRNA. (2506 bp)

misc_feature 496..>573 /locus_tag="AT3G17712" /note="MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; Region: NRDE2_MID; cd22200" /db_xref="CDD:412062" misc_feature 916..2016 /locus_tag="AT3G17712" /note="necessary for RNA interference; Region: NRDE-2; pfam08424" /db_xref="CDD:462472" ORIGIN // REFERENCE 1 (bases 1 to 2506) AUTHORS Salanoubat,M., Lemcke,K., Rieger,M., Ansorge,W., Unseld,M., Fartmann,B., Valle,G., Blocker,H., Perez-Alonso,M., Obermaier,B., Delseny,M., Boutry,M., Grivell,L.A., Mache,R., Puigdomenech,P., De Simone,V., Choisne,N.,...

NM_001202991.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana dicer-like 2 (DCL2), partial mRNA. (4125 bp)

INSD:ES202797.1,INSD:BE524988.1,INSD:ES126577.1, INSD:BE529383.1" /inference="Similar to RNA sequence, mRNA:INSD:DQ479971.1" /note="dicer-like 2 (DCL2); FUNCTIONS IN: in 7 functions; INVOLVED IN: defense response to virus, maintenance of DNA methylation, production of ta-siRNAs involved in RNA interference; LOCATED IN: intracellular; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), Double-stranded RNA-binding (InterPro:IPR001159), Argonaute/Dicer protein, PAZ...

Synonym: ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28
NM_001084632.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana uncharacterized protein (AT3G17712), mRNA. (2653 bp)

misc_feature 531..>608 /locus_tag="AT3G17712" /note="MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; Region: NRDE2_MID; cd22200" /db_xref="CDD:412062" misc_feature 951..2051 /locus_tag="AT3G17712" /note="necessary for RNA interference; Region: NRDE-2; pfam08424" /db_xref="CDD:462472" ORIGIN // REFERENCE 1 (bases 1 to 2653) AUTHORS Salanoubat,M., Lemcke,K., Rieger,M., Ansorge,W., Unseld,M., Fartmann,B., Valle,G., Blocker,H., Perez-Alonso,M., Obermaier,B., Delseny,M., Boutry,M., Grivell,L.A., Mache,R., Puigdomenech,P., De Simone,V., Choisne,N.,...

NM_001202992.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana uncharacterized protein (AT3G17712), mRNA. (2797 bp)

misc_feature 496..>573 /locus_tag="AT3G17712" /note="MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; Region: NRDE2_MID; cd22200" /db_xref="CDD:412062" misc_feature 916..2091 /locus_tag="AT3G17712" /note="necessary for RNA interference; Region: NRDE-2; pfam08424" /db_xref="CDD:462472" ORIGIN // REFERENCE 1 (bases 1 to 2797) AUTHORS Salanoubat,M., Lemcke,K., Rieger,M., Ansorge,W., Unseld,M., Fartmann,B., Valle,G., Blocker,H., Perez-Alonso,M., Obermaier,B., Delseny,M., Boutry,M., Grivell,L.A., Mache,R., Puigdomenech,P., De Simone,V., Choisne,N.,...

NM_001161148.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana nuclear matrix protein-like protein (THO1), mRNA. (2250 bp)

db_xref="Araport:AT5G09860" /db_xref="GeneID:830846" /db_xref="TAIR:AT5G09860" CDS 254..2050 /gene="THO1" /locus_tag="AT5G09860" /gene_synonym="AtHPR1; AtTHO1; HPR1; MYH9.7; MYH9_7" /note="THO1; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: production of ta-siRNAs involved in RNA interference, gene silencing by RNA; LOCATED IN: cellular_component unknown; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: THO complex, subunit THOC1 (InterPro:IPR021861)." /codon_start=1 /product="nuclear matrix protein-like protein" /protein_id="NP...

Synonym: AtHPR1; AtTHO1; HPR1; MYH9.7; MYH9_7
NM_001203340.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana uncharacterized protein (AT3G17740), mRNA. (3811 bp)

misc_feature 460..>537 /locus_tag="AT3G17740" /note="MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; Region: NRDE2_MID; cd22200" /db_xref="CDD:412062" misc_feature 880..2055 /locus_tag="AT3G17740" /note="necessary for RNA interference; Region: NRDE-2; pfam08424" /db_xref="CDD:462472" ORIGIN // REFERENCE 1 (bases 1 to 3811) AUTHORS Salanoubat,M., Lemcke,K., Rieger,M., Ansorge,W., Unseld,M., Fartmann,B., Valle,G., Blocker,H., Perez-Alonso,M., Obermaier,B., Delseny,M., Boutry,M., Grivell,L.A., Mache,R., Puigdomenech,P., De Simone,V., Choisne,N.,...

NM_112655.3 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana SNF2 domain-containing protein / helicase domain-containing protein (DRD1), mRNA. (3104 bp)

INSD:ES034363.1,INSD:EL098697.1, INSD:BE525817.1,INSD:CB518291.1,INSD:ES038960.1" /note="DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1); FUNCTIONS IN: helicase activity, DNA binding, ATP binding, nucleic acid binding; INVOLVED IN: DNA methylation, production of siRNA involved in RNA interference; LOCATED IN: cellular_component unknown; EXPRESSED IN: 9 plant structures; EXPRESSED DURING: 6 growth stages; CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain...

Synonym: CHR35; DEFECTIVE IN MERISTEM SILENCING 1; DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1; DMS1; F16F14.11; F16F14_11
NM_127193.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana double-stranded-RNA-binding protein 4 (DRB4), mRNA. (1297 bp)

INSD:EH816638.1, INSD:EG519674.1,INSD:EL987543.1" /inference="Similar to RNA sequence, mRNA:INSD:BX823891.1,INSD:AY150509.1" /note="double-stranded-RNA-binding protein 4 (DRB4); FUNCTIONS IN: double-stranded RNA binding, protein binding; INVOLVED IN: production of ta-siRNAs involved in RNA interference; LOCATED IN: nucleus; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Double-stranded RNA-binding (InterPro:IPR001159), Double-stranded RNA-binding-like (InterPro:IPR014720); BEST Arabidopsis thaliana protein match is: dsRNA-binding protein 3...

Synonym: ATTIF3K1; double-stranded-RNA-binding protein 4
NM_202751.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana actin-related protein 4 (ARP4), mRNA. (1721 bp)

of nuclear ARP family of genes. Component of chromatin remodeling complexes, involved in chromatin-mediated gene regulation. Phenotype of the arp4-1 mutant allele revealed partial sterility due to defects in anther development. Targeting the distinct, 3' UTR of AtARP4 transcripts with RNA interference caused a drastic reduction in the level of AtARP4 protein expression, and resulted in strong pleiotropic phenotypes such as altered organization of plant organs, early flowering, delayed flower senescence and high levels of sterility. Western blot analysis and immunolabelling demonstrated a clear...

Synonym: actin-related protein 4; ATARP4; F15H18.8; F15H18_8
NM_101702.4 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana double-stranded-RNA-binding protein 4 (DRB4), mRNA. (1368 bp)

INSD:EL987543.1" /inference="Similar to RNA sequence, mRNA:INSD:BX824065.1,INSD:AY074363.1,INSD:BX822860.1, INSD:AY150509.1" /note="double-stranded-RNA-binding protein 4 (DRB4); FUNCTIONS IN: double-stranded RNA binding, protein binding; INVOLVED IN: production of ta-siRNAs involved in RNA interference; LOCATED IN: nucleus; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Double-stranded RNA-binding (InterPro:IPR001159), Double-stranded RNA-binding-like (InterPro:IPR014720); BEST Arabidopsis thaliana protein match is: dsRNA-binding protein 3...

Synonym: ATTIF3K1; double-stranded-RNA-binding protein 4
NM_116145.4 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana separase (ESP), partial mRNA. (6812 bp)

ferredoxin domain that is not present in the proteins of other organisms. Also contains a putative EF-hand calcium binding domain. Mutant seeds exhibited embryo arrest at the globular stage. The endosperm also exhibited a weak titan-like phenotype. Transgenic plants expressing AESP RNA interference (RNAi) from the meiosis-specific DMC1 promoter exhibited alterations in chromosome segregation during meiosis I and II that resulted in polyads containing from one to eight microspores. Plays an essential role in embryo development. Required for the removal of cohesin from meiotic chromosomes and...

Synonym: AESP; EXTRA SPINDLE POLES; F7H19.150; F7H19_150; homolog of separase; RADIALLY SWOLLEN 4; RSW4; SEPARASE
NM_001341570.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana separase (ESP), mRNA. (6954 bp)

Synonym: AESP; EXTRA SPINDLE POLES; F7H19.150; F7H19_150; homolog of separase; RADIALLY SWOLLEN 4; RSW4; SEPARASE
NM_001203875.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana separase (ESP), mRNA. (6907 bp)

Synonym: AESP; EXTRA SPINDLE POLES; F7H19.150; F7H19_150; homolog of separase; RADIALLY SWOLLEN 4; RSW4; SEPARASE
NM_118426.4 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana dicer-like 2 (DCL2), mRNA. (3700 bp)

DCL2" /locus_tag="AT3G03300" /gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28" /note="PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a...; Region: PAZ; cl00301" /db_xref="CDD:469713" misc_feature order(1990..1992,2065..2067,2077..2079,2131..2133, 2209..2211,2215..2217) /gene="DCL2" /locus_tag="AT3G03300" /gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28" /note="nucleic...

Synonym: ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28
NM_001337464.1 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana dicer-like 2 (DCL2), mRNA. (4628 bp)

AT3G03300" CDS 322..4488 /gene="DCL2" /locus_tag="AT3G03300" /gene_synonym="ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28" /note="dicer-like 2 (DCL2); FUNCTIONS IN: in 7 functions; INVOLVED IN: defense response to virus, maintenance of DNA methylation, production of ta-siRNAs involved in RNA interference; LOCATED IN: intracellular; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), Double-stranded RNA-binding (InterPro:IPR001159), Argonaute/Dicer protein, PAZ (InterPro:...

Synonym: ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28
NM_001202869.2 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Arabidopsis thaliana dicer-like 2 (DCL2), mRNA. (4824 bp)

INSD:ES202797.1,INSD:ES126577.1, INSD:ES158551.1,INSD:BE529383.1" /inference="Similar to RNA sequence, mRNA:INSD:DQ479970.1" /note="dicer-like 2 (DCL2); FUNCTIONS IN: in 7 functions; INVOLVED IN: defense response to virus, maintenance of DNA methylation, production of ta-siRNAs involved in RNA interference; LOCATED IN: intracellular; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA/RNA helicase, DEAD/DEAH box type, N-terminal (InterPro:IPR011545), Double-stranded RNA-binding (InterPro:IPR001159), Argonaute/Dicer protein, PAZ (InterPro:...

Synonym: ATDCL2; dicer-like 2; DICER-LIKE 2; T17B22.28
NM_111200.5 - Arabidopsis thaliana (thale cress) - NCBI - TAIR

Data Export:

Debug Info:

0.000 | 0.000 | search_start;
0.080 | 0.080 | count_done; http://172.18.8.71:7700/v1/refsub/query?q=((full_search:*:RNA+interference)%7C(nt:RNA+interference)%7C(aa:RNA+interference))?source=Arabidopsis thaliana (thale cress)?to=0&format=json
0.141 | 0.060 | search_done; http://172.18.8.71:7700/v1/refsub/query?q=((full_search:*:RNA+interference)%7C(nt:RNA+interference)%7C(aa:RNA+interference))?source=Arabidopsis thaliana (thale cress)?to=49?from=0?snippet=full_search?drilldown=source?get=accession,version,gi,length,symbol,synonym,geneid,division,source,definition&format=json
0.143 | 0.002 | cgi_end;

If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]

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