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Entry version 113 (07 Apr 2021)
Sequence version 1 (11 Oct 2004)
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Protein

General transcription and DNA repair factor IIH subunit TFB2

Gene

TFB2

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 transcript 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

Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre-initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module CAK controls the initiation of transcription.

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 processDNA damage, DNA repair, Transcription, Transcription regulation

<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%5Fand%5Ftaxonomy%5Fsection">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:
General transcription and DNA repair factor IIH subunit TFB2Curated
Short name:
AtTFB21 Publication
Short name:
TFIIH subunit TFB2Curated
Alternative name(s):
RNA polymerase II transcription factor B subunit 2Curated
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:TFB2Curated
Synonyms:GTF2H4Curated
Ordered Locus Names:At4g17020Imported
ORF Names:dl4540cImported
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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)Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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 4

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT4G17020

<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

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_00004354351 – 452General transcription and DNA repair factor IIH subunit TFB2Add BLAST452

Proteomic databases

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

More...
PaxDbi
Q680U9

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
234173 [Q680U9-1]

<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
Q680U9, baseline and differential

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the 7-subunit TFIIH core complex composed of XPB, XPD, TFB1/GTF2H1, GTF2H2/P44, TFB4/GTF2H3, TFB2/GTF2H4 and TFB5/GTF2H5, which is active in NER. The core complex associates with the 3-subunit CDK-activating kinase (CAK) module composed of CYCH1/cyclin H1, CDKD and MAT1/At4g30820 to form the 10-subunit holoenzyme (holo-TFIIH) active in transcription.

By similarity1 Publication

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
Q680U9, 3 interactors

STRING: functional protein association networks

More...
STRINGi
3702.AT4G17020.3

<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
Q680U9

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

Belongs to the TFB2 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG3471, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_027280_4_0_1

Identification of Orthologs from Complete Genome Data

More...
OMAi
YLEQYAH

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q680U9

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR040662, Tfb2_C
IPR004598, TFIIH_p52/Tfb2

The PANTHER Classification System

More...
PANTHERi
PTHR13152, PTHR13152, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03849, Tfb2, 1 hit
PF18307, Tfb2_C, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00625, tfb2, 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%5Flength">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>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

This entry describes 1 <p>This subsection of the 'Sequence' section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoform i produced by alternative splicing. AlignAdd to basket
Note: A number of isoforms are produced. According to EST sequences.Curated

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q680U9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MPQVKIIAKN FMDMVASLPA IKLDKLYNNV FICEAILRSL PPLAKKYVLQ
60 70 80 90 100
MLYIDVPVPA TMMEEWVLAD GTSKHRVAID RLIQLRIFSE ISDRKRGTSY
110 120 130 140 150
SLNPTFQNNL QKHIISGGVL PREPMNSDNA IKLPSLQELE TYALKQWECF
160 170 180 190 200
LLQLINSGQG EKLTGISSSM MKIFQRGLLS QRDKDGPRLT ESGFQFLLMD
210 220 230 240 250
TNAQLWYIIR EYILNAEERD VDPADLISFL LELSFHVTGQ AYNLNTLTEV
260 270 280 290 300
QNNTLKDLAD LGLVKLQQGR KDSWFIPTKL ATNLSVSLAD SSARKEGFVV
310 320 330 340 350
METNFRMYAY STSKLQCEIL RLFARIEYQL PNLIACAITK ESLYNAFDNG
360 370 380 390 400
ITSDQIITFL QQNSHPRCAD RVPSIPENVT DQIRLWETDL QRIEMTQAHF
410 420 430 440 450
YDEFPSKDVF EAACDFAREW RGLLWEDSKR MRLVVKSEVH NQMREFLHTQ

SR
Length:452
Mass (Da):52,070
Last modified:October 11, 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:iDC1D1A2A126E4C47
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F4JND0F4JND0_ARATH
RNA polymerase II transcription fac...
At4g17020, Dl4540c, FCAALL.340
482Annotation score:

Annotation score:1 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>
F4JNC9F4JNC9_ARATH
RNA polymerase II transcription fac...
At4g17020, Dl4540c, FCAALL.340
462Annotation score:

Annotation score:1 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>

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence CAB10482 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAB80973 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti348D → G in BAD43671 (Ref. 4) Curated1

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
Z97342 Genomic DNA Translation: CAB10482.1 Sequence problems.
AL161545 Genomic DNA Translation: CAB80973.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE83839.1
AK175768 mRNA Translation: BAD43531.1
AK175908 mRNA Translation: BAD43671.1
BT029179 mRNA Translation: ABJ17114.1

Protein sequence database of the Protein Information Resource

More...
PIRi
E71438

NCBI Reference Sequences

More...
RefSeqi
NP_193435.2, NM_117806.4 [Q680U9-1]

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G17020.1; AT4G17020.1; AT4G17020 [Q680U9-1]

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
827410

Gramene; a comparative resource for plants

More...
Gramenei
AT4G17020.1; AT4G17020.1; AT4G17020 [Q680U9-1]

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT4G17020

Keywords - Coding sequence diversityi

Alternative splicing

<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
Z97342 Genomic DNA Translation: CAB10482.1 Sequence problems.
AL161545 Genomic DNA Translation: CAB80973.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE83839.1
AK175768 mRNA Translation: BAD43531.1
AK175908 mRNA Translation: BAD43671.1
BT029179 mRNA Translation: ABJ17114.1
PIRiE71438
RefSeqiNP_193435.2, NM_117806.4 [Q680U9-1]

3D structure databases

SMRiQ680U9
ModBaseiSearch...

Protein-protein interaction databases

IntActiQ680U9, 3 interactors
STRINGi3702.AT4G17020.3

Proteomic databases

PaxDbiQ680U9
ProteomicsDBi234173 [Q680U9-1]

Genome annotation databases

EnsemblPlantsiAT4G17020.1; AT4G17020.1; AT4G17020 [Q680U9-1]
GeneIDi827410
GrameneiAT4G17020.1; AT4G17020.1; AT4G17020 [Q680U9-1]
KEGGiath:AT4G17020

Organism-specific databases

AraportiAT4G17020

Phylogenomic databases

eggNOGiKOG3471, Eukaryota
HOGENOMiCLU_027280_4_0_1
OMAiYLEQYAH
PhylomeDBiQ680U9

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q680U9

Gene expression databases

ExpressionAtlasiQ680U9, baseline and differential

Family and domain databases

InterProiView protein in InterPro
IPR040662, Tfb2_C
IPR004598, TFIIH_p52/Tfb2
PANTHERiPTHR13152, PTHR13152, 1 hit
PfamiView protein in Pfam
PF03849, Tfb2, 1 hit
PF18307, Tfb2_C, 1 hit
TIGRFAMsiTIGR00625, tfb2, 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 nameiTFB2_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: Q680U9
Secondary accession number(s): O23546, Q680F9
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 17, 2016
Last sequence update: October 11, 2004
Last modified: April 7, 2021
This is version 113 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

Reference proteome

Documents

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