Human Gene GTF2B (uc001dmo.4) Description and Page Index
  Description: Homo sapiens general transcription factor IIB (GTF2B), mRNA.
RefSeq Summary (NM_001514): This gene encodes the general transcription factor IIB, one of the ubiquitous factors required for transcription initiation by RNA polymerase II. The protein localizes to the nucleus where it forms a complex (the DAB complex) with transcription factors IID and IIA. Transcription factor IIB serves as a bridge between IID, the factor which initially recognizes the promoter sequence, and RNA polymerase II. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.635150.1, SRR1660803.151351.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000370500.10/ ENSP00000359531.5 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:89,318,321-89,357,301 Size: 38,981 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:89,318,896-89,357,182 Size: 38,287 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:89,318,321-89,357,301)mRNA (may differ from genome)Protein (316 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TF2B_HUMAN
DESCRIPTION: RecName: Full=Transcription initiation factor IIB; AltName: Full=General transcription factor TFIIB; AltName: Full=S300-II;
FUNCTION: General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.
COFACTOR: Binds 1 zinc ion per subunit.
SUBUNIT: Associates with TFIID-IIA (DA complex) to form TFIID-IIA- IIB (DAB-complex) which is then recognized by polymerase II. Interacts with the transcription elongation factor TCEA2. Interacts with HIV-1 Vpr. Interacts with GPBP1 (By similarity). Interacts with Epstein-Barr virus EBNA2.
INTERACTION: P46077:GRF4 (xeno); NbExp=2; IntAct=EBI-389564, EBI-637479;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the TFIIB family.
SIMILARITY: Contains 1 TFIIB-type zinc finger.

-  MalaCards Disease Associations
  MalaCards Gene Search: GTF2B
Diseases sorted by gene-association score: herpes simplex (5), familial atrial fibrillation (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.28 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 485.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.30119-0.339 Picture PostScript Text
3' UTR -125.51575-0.218 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013763 - Cyclin-like
IPR000812 - TFIIB
IPR023486 - TFIIB_CS
IPR013150 - TFIIB_cyclin
IPR013137 - Znf_TFIIB

Pfam Domains:
PF00134 - Cyclin, N-terminal domain
PF00382 - Transcription factor TFIIB repeat
PF08271 - TFIIB zinc-binding

SCOP Domains:
47954 - Cyclin-like
57783 - Zinc beta-ribbon

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1C9B
- X-ray MuPIT

1DL6
- NMR MuPIT

1RLY
- NMR MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
1RO4 - NMR MuPIT 1TFB - NMR MuPIT 1VOL - X-ray MuPIT
2PHG - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q00403
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding
GO:0000993 RNA polymerase II core binding
GO:0001047 core promoter binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0008270 zinc ion binding
GO:0016407 acetyltransferase activity
GO:0017025 TBP-class protein binding
GO:0046872 metal ion binding
GO:0046966 thyroid hormone receptor binding
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0001174 transcriptional start site selection at RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006473 protein acetylation
GO:0016032 viral process
GO:0042795 snRNA transcription from RNA polymerase II promoter
GO:0043923 positive regulation by host of viral transcription
GO:0050434 positive regulation of viral transcription
GO:0051123 RNA polymerase II transcriptional preinitiation complex assembly
GO:0060261 positive regulation of transcription initiation from RNA polymerase II promoter
GO:0070897 DNA-templated transcriptional preinitiation complex assembly
GO:1904798 positive regulation of core promoter binding
GO:1990114 RNA Polymerase II core complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005669 transcription factor TFIID complex
GO:0005694 chromosome
GO:0016604 nuclear body
GO:0032993 protein-DNA complex
GO:0090575 RNA polymerase II transcription factor complex
GO:0097550 transcriptional preinitiation complex


-  Descriptions from all associated GenBank mRNAs
  AK289822 - Homo sapiens cDNA FLJ75997 complete cds, highly similar to Homo sapiens general transcription factor IIB (GTF2B), mRNA.
BC021000 - Homo sapiens general transcription factor IIB, mRNA (cDNA clone IMAGE:3832905).
FW340047 - Screening.
BC020597 - Homo sapiens general transcription factor IIB, mRNA (cDNA clone MGC:22152 IMAGE:4807599), complete cds.
M76766 - Human transcription factor (TFIIB) mRNA, complete cds.
S44184 - S300-II=transcription factor [human, mRNA Partial, 1222 nt].
X59268 - Human mRNA for general transcription factor IIB.
JD434585 - Sequence 415609 from Patent EP1572962.
JD486357 - Sequence 467381 from Patent EP1572962.
JD036357 - Sequence 17381 from Patent EP1572962.
AB451296 - Homo sapiens GTF2B mRNA for general transcription factor IIB, complete cds, clone: FLJ08145AAAN.
KJ891312 - Synthetic construct Homo sapiens clone ccsbBroadEn_00706 GTF2B gene, encodes complete protein.
EU446894 - Synthetic construct Homo sapiens clone IMAGE:100070248; IMAGE:100012103; FLH258182.01L general transcription factor IIB (GTF2B) gene, encodes complete protein.
AB587461 - Synthetic construct DNA, clone: pF1KB8232, Homo sapiens GTF2B gene for general transcription factor IIB, without stop codon, in Flexi system.
CU676570 - Synthetic construct Homo sapiens gateway clone IMAGE:100022206 5' read GTF2B mRNA.
AX721092 - Sequence 52 from Patent WO0220754.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03022 - Basal transcription factors

Reactome (by CSHL, EBI, and GO)

Protein Q00403 (Reactome details) participates in the following event(s):

R-HSA-109637 Binding of TFIIA and TFIIB to the pol II promoter:TFIID complex
R-HSA-6810234 General transcription factors bind SNAPc:POU2F1:ZNF143:snRNA gene
R-HSA-73946 Abortive initiation
R-HSA-75856 Abortive Initiation Before Second Transition
R-HSA-167474 Abortive HIV-1 Initiation Before Second Transition
R-HSA-167477 Abortive HIV-1 initiation after formation of the first phosphodiester bond
R-HSA-75866 Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP
R-HSA-75861 NTP Binds Active Site of RNA Polymerase II
R-HSA-75864 Newly Formed Phosphodiester Bond Stabilized and PPi Released
R-HSA-109638 Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex
R-HSA-75862 Fall Back to Closed Pre-initiation Complex
R-HSA-75949 RNA Polymerase II Promoter Opening: First Transition
R-HSA-167134 Newly formed phosphodiester bond stabilized and PPi released
R-HSA-167130 Nucleophillic attack by 3'-hydroxyl oxygen of nascent HIV-1 transcript on the Alpha phosphate of NTP
R-HSA-167118 NTP binds active site of RNA Polymerase II in HIV-1 open pre-initiation complex
R-HSA-167484 Fall Back to Closed Pre-initiation Complex
R-HSA-167097 HIV Promoter Opening: First Transition
R-HSA-6810238 RNA polymerase II binds initiation factors at promoter of snRNA gene (U1, U2, U4, U4atac, U5, U11, U12)
R-HSA-75095 Binding of TFIIE to the growing preinitiation complex
R-HSA-6810235 RPAP2 binds RNA polymerase II phosphorylated at serine-7 residues of heptad repeats in the C-terminal domain
R-HSA-6810233 CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter
R-HSA-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA
R-HSA-109639 Formation of the closed pre-initiation complex
R-HSA-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-HSA-6807505 RNA polymerase II transcribes snRNA genes
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-73776 RNA Polymerase II Promoter Escape
R-HSA-167162 RNA Polymerase II HIV Promoter Escape
R-HSA-167161 HIV Transcription Initiation
R-HSA-75953 RNA Polymerase II Transcription Initiation
R-HSA-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-HSA-167172 Transcription of the HIV genome
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-74160 Gene expression (Transcription)
R-HSA-162587 HIV Life Cycle
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1A7, NM_001514, NP_001505, Q00403, Q5JS30, TF2B, TF2B_HUMAN, TFIIB
UCSC ID: uc001dmo.4
RefSeq Accession: NM_001514
Protein: Q00403 (aka TF2B_HUMAN)
CCDS: CCDS715.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001514.5
exon count: 7CDS single in 3' UTR: no RNA size: 1651
ORF size: 951CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 2102.00frame shift in genome: no % Coverage: 99.64
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.