Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Entry version 92 (02 Dec 2020)
Sequence version 1 (24 May 2005)
Previous versions | rss
Add a publicationFeedback
Protein

DNA-directed RNA polymerase II subunit rpb4

Gene

polr2d

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score:

Annotation score:4 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>
-Protein inferred from homologyi <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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity).

By similarity

<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

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-DDI-113418, Formation of the Early Elongation Complex
R-DDI-674695, RNA Polymerase II Pre-transcription Events
R-DDI-6781823, Formation of TC-NER Pre-Incision Complex
R-DDI-6782135, Dual incision in TC-NER
R-DDI-6782210, Gap-filling DNA repair synthesis and ligation in TC-NER
R-DDI-6796648, TP53 Regulates Transcription of DNA Repair Genes
R-DDI-6803529, FGFR2 alternative splicing
R-DDI-6807505, RNA polymerase II transcribes snRNA genes
R-DDI-72086, mRNA Capping
R-DDI-72163, mRNA Splicing - Major Pathway
R-DDI-72165, mRNA Splicing - Minor Pathway
R-DDI-73776, RNA Polymerase II Promoter Escape
R-DDI-73779, RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-DDI-75953, RNA Polymerase II Transcription Initiation
R-DDI-75955, RNA Polymerase II Transcription Elongation
R-DDI-76042, RNA Polymerase II Transcription Initiation And Promoter Clearance
R-DDI-77075, RNA Pol II CTD phosphorylation and interaction with CE
R-DDI-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
Recommended name:
DNA-directed RNA polymerase II subunit rpb4
Short name:
RNA polymerase II subunit B4
Alternative name(s):
DNA-directed RNA polymerase II subunit D
<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:polr2d
Synonyms:rpb4
ORF Names:DDB_G0282739
<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>OrganismiDictyostelium discoideum (Slime mold)
<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 identifieri44689 [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 lineageiEukaryotaAmoebozoaEvoseaEumycetozoaDictyosteliaDictyostelialesDictyosteliaceaeDictyostelium
<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
  • UP000002195 <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> Componentsi: Chromosome 3, Unassembled WGS sequence

Organism-specific databases

Dictyostelium discoideum online informatics resource

More...
dictyBasei
DDB_G0282739, rpb4

<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

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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003294311 – 155DNA-directed RNA polymerase II subunit rpb4Add BLAST155

Proteomic databases

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

More...
PaxDbi
Q54S04

<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 (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex (By similarity).

By similarity

GO - Molecular functioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
44689.DDB0216294

<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

More...
SMRi
Q54S04

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
KOG2351, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_110332_2_1_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q54S04

Identification of Orthologs from Complete Genome Data

More...
OMAi
HRKTQNE

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q54S04

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.

Q54S04-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTDPLIKRSG IQEEEDLTTL KFPRDLKDAK FLLNSEVAIL LEHRKGISES
60 70 80 90 100
EGTEFPQNTL LIHLYYNSIN DIIRTFHKTL AYAEKFSRYK NKTSIKQVRT
110 120 130 140 150
ALSKQNLEEF EIASLANLCP EISDEAKSLI PSLKKMEDDE LQAILDELSN

LRKFN
Length:155
Mass (Da):17,889
Last modified:May 24, 2005 - 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:iEC6754553CF07C70
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AAFI02000047 Genomic DNA Translation: EAL66229.1

NCBI Reference Sequences

More...
RefSeqi
XP_640235.1, XM_635143.1

Genome annotation databases

Ensembl protists genome annotation project

More...
EnsemblProtistsi
EAL66229; EAL66229; DDB_G0282739

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
8623774

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ddi:DDB_G0282739

<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
AAFI02000047 Genomic DNA Translation: EAL66229.1
RefSeqiXP_640235.1, XM_635143.1

3D structure databases

SMRiQ54S04
ModBaseiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0216294

Proteomic databases

PaxDbiQ54S04

Genome annotation databases

EnsemblProtistsiEAL66229; EAL66229; DDB_G0282739
GeneIDi8623774
KEGGiddi:DDB_G0282739

Organism-specific databases

dictyBaseiDDB_G0282739, rpb4

Phylogenomic databases

eggNOGiKOG2351, Eukaryota
HOGENOMiCLU_110332_2_1_1
InParanoidiQ54S04
OMAiHRKTQNE
PhylomeDBiQ54S04

Enzyme and pathway databases

ReactomeiR-DDI-113418, Formation of the Early Elongation Complex
R-DDI-674695, RNA Polymerase II Pre-transcription Events
R-DDI-6781823, Formation of TC-NER Pre-Incision Complex
R-DDI-6782135, Dual incision in TC-NER
R-DDI-6782210, Gap-filling DNA repair synthesis and ligation in TC-NER
R-DDI-6796648, TP53 Regulates Transcription of DNA Repair Genes
R-DDI-6803529, FGFR2 alternative splicing
R-DDI-6807505, RNA polymerase II transcribes snRNA genes
R-DDI-72086, mRNA Capping
R-DDI-72163, mRNA Splicing - Major Pathway
R-DDI-72165, mRNA Splicing - Minor Pathway
R-DDI-73776, RNA Polymerase II Promoter Escape
R-DDI-73779, RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-DDI-75953, RNA Polymerase II Transcription Initiation
R-DDI-75955, RNA Polymerase II Transcription Elongation
R-DDI-76042, RNA Polymerase II Transcription Initiation And Promoter Clearance
R-DDI-77075, RNA Pol II CTD phosphorylation and interaction with CE
R-DDI-9018519, Estrogen-dependent gene expression

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q54S04

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

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 nameiRPB4_DICDI
<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: Q54S04
<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: April 8, 2008
Last sequence update: May 24, 2005
Last modified: December 2, 2020
This is version 92 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)

<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

Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again