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Entry version 118 (08 May 2019)
Sequence version 1 (01 May 2000)
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Protein

Transcription elongation factor SPT4

Gene

spt-4

Organism
Caenorhabditis elegans
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>
-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

May function as a component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates transcription elongation by RNA polymerase II. DSIF may enhance transcriptional pausing at sites proximal to the promoter, which may in turn facilitate the assembly of an elongation competent RNA polymerase II complex.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri15 – 35C4-typeSequence analysisAdd BLAST21

<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

Molecular functionActivator, Repressor
Biological processTranscription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-CEL-112382 Formation of RNA Pol II elongation complex
R-CEL-113418 Formation of the Early Elongation Complex
R-CEL-674695 RNA Polymerase II Pre-transcription Events
R-CEL-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-CEL-75955 RNA Polymerase II Transcription Elongation

<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:
Transcription elongation factor SPT4
Alternative name(s):
DRB sensitivity-inducing factor small subunit
Short name:
DSIF small subunit
<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:spt-4
ORF Names:F54C4.2
<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>OrganismiCaenorhabditis elegans
<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 identifieri6239 [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 lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditinaRhabditomorphaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
<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
  • UP000001940 <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 III

Organism-specific databases

WormBase

More...
WormBasei
F54C4.2 ; CE19891 ; WBGene00005014 ; spt-4

<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

Keywords - Cellular componenti

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_00002103341 – 120Transcription elongation factor SPT4Add BLAST120

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
Q9TZ93

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

More...
PaxDbi
Q9TZ93

PeptideAtlas

More...
PeptideAtlasi
Q9TZ93

PRoteomics IDEntifications database

More...
PRIDEi
Q9TZ93

<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
WBGene00005014 Expressed in 5 organ(s), highest expression level in multi-cellular organism

<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

Interacts with spt-5 to form DSIF. DSIF interacts with RNA polymerase II and with the positive transcription elongation factor b complex (P-TEFb complex), which is composed of cdk-9 and cyclin-T (cit-1.1 or cit-1.2) (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
40448, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-25841N

STRING: functional protein association networks

More...
STRINGi
6239.F54C4.2

<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
Q9TZ93

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 39Interaction with spt-5By similarityAdd BLAST39

<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

Belongs to the SPT4 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri15 – 35C4-typeSequence analysisAdd BLAST21

Keywords - Domaini

Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG3490 Eukaryota
COG5204 LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00390000018559

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000172685

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q9TZ93

KEGG Orthology (KO)

More...
KOi
K15171

Identification of Orthologs from Complete Genome Data

More...
OMAi
VRGMYAV

Database of Orthologous Groups

More...
OrthoDBi
1617752at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9TZ93

Family and domain databases

Conserved Domains Database

More...
CDDi
cd07973 Spt4, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.40.210, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR029040 RPABC4/Spt4
IPR009287 Spt4
IPR022800 Spt4/RpoE2_Znf
IPR038510 Spt4_sf

The PANTHER Classification System

More...
PANTHERi
PTHR12882 PTHR12882, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF06093 Spt4, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF025023 Spt4, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01389 Spt4, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF63393 SSF63393, 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>.<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.

Q9TZ93-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSASVPADLR NLRACLLCSL VKSVESFQKE GCENCEDVLH LKGDEEKVYD
60 70 80 90 100
CTSANYDGMI AAMSNNESWV CKWQKMQRKV KGMYAISVSG VLPNNIVSEL
110 120
KSLGVRYKPN QRDYSTQFKK
Length:120
Mass (Da):13,536
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:iE48D2A78789D5467
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
FO080712 Genomic DNA Translation: CCD66087.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T33605

NCBI Reference Sequences

More...
RefSeqi
NP_497135.1, NM_064734.4

Genome annotation databases

Ensembl metazoan genome annotation project

More...
EnsemblMetazoai
F54C4.2; F54C4.2; WBGene00005014

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
175172

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
cel:CELE_F54C4.2

UCSC genome browser

More...
UCSCi
F54C4.2 c. elegans

<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
FO080712 Genomic DNA Translation: CCD66087.1
PIRiT33605
RefSeqiNP_497135.1, NM_064734.4

3D structure databases

SMRiQ9TZ93
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi40448, 1 interactor
DIPiDIP-25841N
STRINGi6239.F54C4.2

Proteomic databases

EPDiQ9TZ93
PaxDbiQ9TZ93
PeptideAtlasiQ9TZ93
PRIDEiQ9TZ93

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiF54C4.2; F54C4.2; WBGene00005014
GeneIDi175172
KEGGicel:CELE_F54C4.2
UCSCiF54C4.2 c. elegans

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
175172
WormBaseiF54C4.2 ; CE19891 ; WBGene00005014 ; spt-4

Phylogenomic databases

eggNOGiKOG3490 Eukaryota
COG5204 LUCA
GeneTreeiENSGT00390000018559
HOGENOMiHOG000172685
InParanoidiQ9TZ93
KOiK15171
OMAiVRGMYAV
OrthoDBi1617752at2759
PhylomeDBiQ9TZ93

Enzyme and pathway databases

ReactomeiR-CEL-112382 Formation of RNA Pol II elongation complex
R-CEL-113418 Formation of the Early Elongation Complex
R-CEL-674695 RNA Polymerase II Pre-transcription Events
R-CEL-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-CEL-75955 RNA Polymerase II Transcription Elongation

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9TZ93

Gene expression databases

BgeeiWBGene00005014 Expressed in 5 organ(s), highest expression level in multi-cellular organism

Family and domain databases

CDDicd07973 Spt4, 1 hit
Gene3Di3.30.40.210, 1 hit
InterProiView protein in InterPro
IPR029040 RPABC4/Spt4
IPR009287 Spt4
IPR022800 Spt4/RpoE2_Znf
IPR038510 Spt4_sf
PANTHERiPTHR12882 PTHR12882, 1 hit
PfamiView protein in Pfam
PF06093 Spt4, 1 hit
PIRSFiPIRSF025023 Spt4, 1 hit
SMARTiView protein in SMART
SM01389 Spt4, 1 hit
SUPFAMiSSF63393 SSF63393, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
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 nameiSPT4H_CAEEL
<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: Q9TZ93
<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: November 22, 2005
Last sequence update: May 1, 2000
Last modified: May 8, 2019
This is version 118 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 programCaenorhabditis annotation project

<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. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
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