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Entry version 109 (16 Oct 2019)
Sequence version 1 (16 Aug 2004)
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Protein
Submitted name:

Polr2d protein

Gene

polr2d

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Unreviewed-Annotation score:

Annotation score:2 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

<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

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DRE-112382 Formation of RNA Pol II elongation complex
R-DRE-113418 Formation of the Early Elongation Complex
R-DRE-5578749 Transcriptional regulation by small RNAs
R-DRE-674695 RNA Polymerase II Pre-transcription Events
R-DRE-6781823 Formation of TC-NER Pre-Incision Complex
R-DRE-6782135 Dual incision in TC-NER
R-DRE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-DRE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-DRE-6807505 RNA polymerase II transcribes snRNA genes
R-DRE-72086 mRNA Capping
R-DRE-72163 mRNA Splicing - Major Pathway
R-DRE-72165 mRNA Splicing - Minor Pathway
R-DRE-72203 Processing of Capped Intron-Containing Pre-mRNA
R-DRE-73776 RNA Polymerase II Promoter Escape
R-DRE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-DRE-75953 RNA Polymerase II Transcription Initiation
R-DRE-75955 RNA Polymerase II Transcription Elongation
R-DRE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-DRE-77075 RNA Pol II CTD phosphorylation and interaction with CE
R-DRE-9018519 Estrogen-dependent gene expression

<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
Submitted name:
Polr2d proteinImported
Submitted name:
Polymerase (RNA) II (DNA directed) polypeptide DImported
Submitted name:
RNA polymerase II subunit DImported
<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:polr2dImported
<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>OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)Imported
<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 identifieri7955 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
<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
  • UP000000437 <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

Zebrafish Information Network genome database

More...
ZFINi
ZDB-GENE-040714-2 polr2d

<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 Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

<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

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSDARG00000076509 Expressed in 17 organ(s), highest expression level in mature ovarian follicle

<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

GO - Molecular functioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
7955.ENSDARP00000099022

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini23 – 140RPOL4cInterPro annotationAdd BLAST118

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2351 Eukaryota
COG5250 LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00390000004912

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000195281

Identification of Orthologs from Complete Genome Data

More...
OMAi
HRKTQNE

TreeFam database of animal gene trees

More...
TreeFami
TF103039

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.20.1250.40, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR010997 HRDC-like_sf
IPR006590 RNA_pol_Rpb4/RPC9_core
IPR005574 RPB4/RPC9
IPR038324 Rpb4/RPC9_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03874 RNA_pol_Rpb4, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00657 RPOL4c, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47819 SSF47819, 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.

Q6DRG4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAAAGATQVG DVEEDASQLM FPKEFENAET LLNSEVHMLL EHRKQQNESA
60 70 80 90 100
EDEQELSEVF MKTLNYTARF SRFKNRETIA SVRSLLLQKK LHKFELASLA
110 120 130 140
NLCPEAAEEA KALIPSLEGR FEDEELQQIL DDIQTKRSFQ Y
Length:141
Mass (Da):16,167
Last modified:August 16, 2004 - 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:i2F0D552BE280C13C
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CU638696 Genomic DNA No translation available.
BC095261 mRNA Translation: AAH95261.1
BC164278 mRNA Translation: AAI64278.1
AY648795 mRNA Translation: AAT68113.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSDART00000108718; ENSDARP00000099022; ENSDARG00000076509

<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
CU638696 Genomic DNA No translation available.
BC095261 mRNA Translation: AAH95261.1
BC164278 mRNA Translation: AAI64278.1
AY648795 mRNA Translation: AAT68113.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000099022

Genome annotation databases

EnsembliENSDART00000108718; ENSDARP00000099022; ENSDARG00000076509

Organism-specific databases

ZFINiZDB-GENE-040714-2 polr2d

Phylogenomic databases

eggNOGiKOG2351 Eukaryota
COG5250 LUCA
GeneTreeiENSGT00390000004912
HOGENOMiHOG000195281
OMAiHRKTQNE
TreeFamiTF103039

Enzyme and pathway databases

ReactomeiR-DRE-112382 Formation of RNA Pol II elongation complex
R-DRE-113418 Formation of the Early Elongation Complex
R-DRE-5578749 Transcriptional regulation by small RNAs
R-DRE-674695 RNA Polymerase II Pre-transcription Events
R-DRE-6781823 Formation of TC-NER Pre-Incision Complex
R-DRE-6782135 Dual incision in TC-NER
R-DRE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-DRE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-DRE-6807505 RNA polymerase II transcribes snRNA genes
R-DRE-72086 mRNA Capping
R-DRE-72163 mRNA Splicing - Major Pathway
R-DRE-72165 mRNA Splicing - Minor Pathway
R-DRE-72203 Processing of Capped Intron-Containing Pre-mRNA
R-DRE-73776 RNA Polymerase II Promoter Escape
R-DRE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-DRE-75953 RNA Polymerase II Transcription Initiation
R-DRE-75955 RNA Polymerase II Transcription Elongation
R-DRE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-DRE-77075 RNA Pol II CTD phosphorylation and interaction with CE
R-DRE-9018519 Estrogen-dependent gene expression

Gene expression databases

BgeeiENSDARG00000076509 Expressed in 17 organ(s), highest expression level in mature ovarian follicle

Family and domain databases

Gene3Di1.20.1250.40, 1 hit
InterProiView protein in InterPro
IPR010997 HRDC-like_sf
IPR006590 RNA_pol_Rpb4/RPC9_core
IPR005574 RPB4/RPC9
IPR038324 Rpb4/RPC9_sf
PfamiView protein in Pfam
PF03874 RNA_pol_Rpb4, 1 hit
SMARTiView protein in SMART
SM00657 RPOL4c, 1 hit
SUPFAMiSSF47819 SSF47819, 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 nameiQ6DRG4_DANRE
<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: Q6DRG4
Secondary accession number(s): F1RDX0
<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/TrEMBL: August 16, 2004
Last sequence update: August 16, 2004
Last modified: October 16, 2019
This is version 109 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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

<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>Keywords - Technical termi

Complete proteome, Proteomics identificationCombined sources, Reference proteomeImported
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