Gene: Sopen03g030070

General Information

Description This gene encodes the second largest, catalytic subunit of the nuclear DNA-dependent RNA polymerase IV (aka RNA polymerase D). The NRPD2 protein is found at nuclear foci that overlap or are adjacent to chromocentromeres but are not fully coincident with chromocentromeres. The loss of NRPD2 leads to the loss of cytosine methylation at pericentromeric 5S genes and AtSN1 retroelements but has no discernible effect on centromere repeat methylation. This suggests that Pol IV primarily affects facultative heterochromatin rather than constitutive heterochromatin. | nuclear RNA polymerase D2A (NRPD2A) | CONTAINS InterPro DOMAIN/s: DNA-directed RNA polymerase, subunit 2, domain 6 , RNA polymerase Rpb2, domain 7 , RNA polymerase, beta subunit, protrusion , RNA polymerase Rpb2, domain 3 , DNA-directed RNA polymerase, subunit 2 , RNA polymerase Rpb2, domain 2 , RNA polymerase Rpb2, domain 4 , RNA polymerase, beta subunit, conserved site , RNA polymerase Rpb2, domain 5 | BEST Arabidopsis thaliana protein match is: nuclear RNA polymerase D2B ., DNA-directed RNA polymerase, subunit 2, domain 6, DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit beta) (RNA polymerase subunit beta) - Mesostigma viride

GO term	Evidence(s)	Provider(s)	Description	Source(s)
GO:0050776	ISO	PLAZA Integrative Orthology	regulation of immune response	AT3G23780
GO:0050832	ISO	PLAZA Integrative Orthology	defense response to fungus	AT3G23780
GO:0030422	ISO	PLAZA Integrative Orthology	production of siRNA involved in RNA interference	AT3G23780
GO:0031047	ISO	PLAZA Integrative Orthology	gene silencing by RNA	AT3G23780
GO:0006306	ISO	PLAZA Integrative Orthology	DNA methylation	AT3G23780
GO:0035194	ISO	PLAZA Integrative Orthology	post-transcriptional gene silencing by RNA	AT3G23780
GO:0016458	ISO	PLAZA Integrative Orthology	gene silencing	AT3G18090
GO:0006351	IEA	InterPro	transcription, DNA-templated

GO term	Evidence(s)	Provider(s)	Description	Source(s)
GO:0005515	ISO	PLAZA Integrative Orthology	protein binding	AT3G23780
GO:0003677	IEA	InterPro	DNA binding
GO:0032549	IEA	InterPro	ribonucleoside binding
GO:0003899	IEA	InterPro	DNA-directed 5'-3' RNA polymerase activity

GO term	Evidence(s)	Provider(s)	Description	Source(s)
GO:0005634	ISO	PLAZA Integrative Orthology	nucleus	AT3G23780
GO:0030880	ISO	PLAZA Integrative Orthology	RNA polymerase complex	AT3G23780
GO:0000792	ISO	PLAZA Integrative Orthology	heterochromatin	AT3G23780
GO:0000418	ISO	PLAZA Integrative Orthology	RNA polymerase IV complex	AT3G23780
GO:0000419	ISO	PLAZA Integrative Orthology	RNA polymerase V complex	AT3G23780

Experimental Evidence

Computational Reviewed Evidence

Electronic Evidence

InterPro	Description
IPR007645	RNA polymerase Rpb2, domain 3
IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily
IPR015712	DNA-directed RNA polymerase, subunit 2
IPR007646	RNA polymerase Rpb2, domain 4
IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain
IPR007641	RNA polymerase Rpb2, domain 7
IPR014724	RNA polymerase Rpb2, OB-fold
IPR007644	RNA polymerase, beta subunit, protrusion
IPR007647	RNA polymerase Rpb2, domain 5
IPR037034	RNA polymerase Rpb2, domain 2 superfamily
IPR007642	RNA polymerase Rpb2, domain 2

Mapman id	Description
15.1.4.2	RNA biosynthesis.DNA-dependent RNA polymerase (Pol) complexes.Pol IV catalytic components.subunit 2
15.1.5.2	RNA biosynthesis.DNA-dependent RNA polymerase (Pol) complexes.Pol V catalytic components.subunit 2