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Entry version 133 (16 Oct 2019)
Sequence version 1 (01 May 2000)
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Protein

DNA-directed RNA polymerases II and V subunit 6B

Gene

NRPB6B

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. Component of RNA polymerase V which mediates RNA-directed DNA methylation-dependent (RdDM) transcriptional gene silencing (TGS) of endogenous repeated sequences, including transposable elements.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processTranscription

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA-directed RNA polymerases II and V subunit 6B
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:NRPB6B
Synonyms:NRPE6B
Ordered Locus Names:At2g04630
ORF Names:F28I8.33
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiArabidopsis thaliana (Mouse-ear cress)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri3702 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000006548 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 2

Organism-specific databases

Arabidopsis Information Portal

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Araporti
AT2G04630

The Arabidopsis Information Resource

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TAIRi
locus:2049213 AT2G04630

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004233231 – 144DNA-directed RNA polymerases II and V subunit 6BAdd BLAST144

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

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PaxDbi
Q9SJ96

PRoteomics IDEntifications database

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PRIDEi
Q9SJ96

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q9SJ96 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9SJ96 AT

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the RNA polymerase II and V complexes.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
407, 9 interactors

Protein interaction database and analysis system

More...
IntActi
Q9SJ96, 8 interactors

STRING: functional protein association networks

More...
STRINGi
3702.AT2G04630.1

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
Q9SJ96

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG3405 Eukaryota
COG1758 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000225272

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
Q9SJ96

KEGG Orthology (KO)

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KOi
K03014

Identification of Orthologs from Complete Genome Data

More...
OMAi
CRYEDEP

Database of Orthologous Groups

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OrthoDBi
1488436at2759

Database for complete collections of gene phylogenies

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PhylomeDBi
Q9SJ96

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.90.940.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00192 RNApol_arch_K, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR020708 DNA-dir_RNA_polK_14-18kDa_CS
IPR006110 Pol_omega/K/RPB6
IPR012293 RNAP_RPB6_omega
IPR028363 RPB6
IPR036161 RPB6/omega-like_sf
IPR006111 RpoK/Rpb6

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01192 RNA_pol_Rpb6, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF500154 RPB6, 1 hit
PIRSF000778 RpoK/RPB6, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01409 RNA_pol_Rpb6, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF63562 SSF63562, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01111 RNA_POL_K_14KD, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q9SJ96-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MADDDYNEVD DLGYEDEPAE PEIEEGVEED ADIKENDDVN VDPLETEDKV
60 70 80 90 100
ETEPVQRPRK TSKFMTKYER ARILGTRALQ ISMNAPVMVE LEGETDPLEI
110 120 130 140
AMKELRQRKI PFTIRRYLPD MSYEEWGVDE LIVEDSWKRQ VGGD
Length:144
Mass (Da):16,740
Last modified:May 1, 2000 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i8210BE0CECE7DE9F
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AC006955 Genomic DNA Translation: AAD22343.1
CP002685 Genomic DNA Translation: AEC05851.1
BT010184 mRNA Translation: AAQ22653.1
AK229481 mRNA Translation: BAF01339.1

Protein sequence database of the Protein Information Resource

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PIRi
E84459

NCBI Reference Sequences

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RefSeqi
NP_178540.1, NM_126492.4

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT2G04630.1; AT2G04630.1; AT2G04630

Database of genes from NCBI RefSeq genomes

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GeneIDi
815006

Gramene; a comparative resource for plants

More...
Gramenei
AT2G04630.1; AT2G04630.1; AT2G04630

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT2G04630

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC006955 Genomic DNA Translation: AAD22343.1
CP002685 Genomic DNA Translation: AEC05851.1
BT010184 mRNA Translation: AAQ22653.1
AK229481 mRNA Translation: BAF01339.1
PIRiE84459
RefSeqiNP_178540.1, NM_126492.4

3D structure databases

SMRiQ9SJ96
ModBaseiSearch...

Protein-protein interaction databases

BioGridi407, 9 interactors
IntActiQ9SJ96, 8 interactors
STRINGi3702.AT2G04630.1

Proteomic databases

PaxDbiQ9SJ96
PRIDEiQ9SJ96

Genome annotation databases

EnsemblPlantsiAT2G04630.1; AT2G04630.1; AT2G04630
GeneIDi815006
GrameneiAT2G04630.1; AT2G04630.1; AT2G04630
KEGGiath:AT2G04630

Organism-specific databases

AraportiAT2G04630
TAIRilocus:2049213 AT2G04630

Phylogenomic databases

eggNOGiKOG3405 Eukaryota
COG1758 LUCA
HOGENOMiHOG000225272
InParanoidiQ9SJ96
KOiK03014
OMAiCRYEDEP
OrthoDBi1488436at2759
PhylomeDBiQ9SJ96

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9SJ96

Gene expression databases

ExpressionAtlasiQ9SJ96 baseline and differential
GenevisibleiQ9SJ96 AT

Family and domain databases

Gene3Di3.90.940.10, 1 hit
HAMAPiMF_00192 RNApol_arch_K, 1 hit
InterProiView protein in InterPro
IPR020708 DNA-dir_RNA_polK_14-18kDa_CS
IPR006110 Pol_omega/K/RPB6
IPR012293 RNAP_RPB6_omega
IPR028363 RPB6
IPR036161 RPB6/omega-like_sf
IPR006111 RpoK/Rpb6
PfamiView protein in Pfam
PF01192 RNA_pol_Rpb6, 1 hit
PIRSFiPIRSF500154 RPB6, 1 hit
PIRSF000778 RpoK/RPB6, 1 hit
SMARTiView protein in SMART
SM01409 RNA_pol_Rpb6, 1 hit
SUPFAMiSSF63562 SSF63562, 1 hit
PROSITEiView protein in PROSITE
PS01111 RNA_POL_K_14KD, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRPB6B_ARATH
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9SJ96
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: May 1, 2000
Last modified: October 16, 2019
This is version 133 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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