Human Gene TAF11 (uc003ojw.2) Description and Page Index
  Description: Homo sapiens TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa (TAF11), transcript variant 1, mRNA.
RefSeq Summary (NM_005643): Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes a small subunit of TFIID that is present in all TFIID complexes and interacts with TBP. This subunit also interacts with another small subunit, TAF13, to form a heterodimer with a structure similar to the histone core structure. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012].
Transcript (Including UTRs)
   Position: hg19 chr6:34,845,555-34,855,848 Size: 10,294 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:34,846,367-34,855,734 Size: 9,368 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:34,845,555-34,855,848)mRNA (may differ from genome)Protein (211 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TAF11_HUMAN
DESCRIPTION: RecName: Full=Transcription initiation factor TFIID subunit 11; AltName: Full=TFIID subunit p30-beta; AltName: Full=Transcription initiation factor TFIID 28 kDa subunit; Short=TAF(II)28; Short=TAFII-28; Short=TAFII28;
FUNCTION: Core TAFII present in both of the previously described TFIID species which either lack or contain TAFII30 (TFIID alpha and TFIID beta respectively).
SUBUNIT: TFIID is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). Interacts with TAF13 both in vitro and intracellularly; also interacts directly with TBP.
INTERACTION: Q15543:TAF13; NbExp=2; IntAct=EBI-1027005, EBI-1026992;
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: TBP and TAFII18 bind to distinct domains of TAFII28.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the TAF11 family.
SEQUENCE CAUTION: Sequence=AAF22038.1; Type=Frameshift; Positions=208;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/taf11/";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TAF11
CDC HuGE Published Literature: TAF11

-  MalaCards Disease Associations
  MalaCards Gene Search: TAF11
Diseases sorted by gene-association score: facioscapulohumeral muscular dystrophy 1 (2)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.20 RPKM in Testis
Total median expression: 938.94 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.70114-0.313 Picture PostScript Text
3' UTR -246.67812-0.304 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
IPR009072 - Histone-fold
IPR006809 - TAFII28

Pfam Domains:
PF00808 - Histone-like transcription factor (CBF/NF-Y) and archaeal histone
PF04719 - hTAFII28-like protein conserved region

SCOP Domains:
47113 - Histone-fold

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

1BH8
- X-ray MuPIT

1BH9
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15544
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-  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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
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 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0042809 vitamin D receptor binding
GO:0046966 thyroid hormone receptor binding
GO:0046982 protein heterodimerization activity
GO:0047485 protein N-terminus binding

Biological Process:
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:0042795 snRNA transcription from RNA polymerase II promoter
GO:0043923 positive regulation by host of viral transcription
GO:0051123 RNA polymerase II transcriptional preinitiation complex assembly
GO:1901796 regulation of signal transduction by p53 class mediator

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005669 transcription factor TFIID complex
GO:0005794 Golgi apparatus


-  Descriptions from all associated GenBank mRNAs
  LF210764 - JP 2014500723-A/18267: Polycomb-Associated Non-Coding RNAs.
BX538195 - Homo sapiens mRNA; cDNA DKFZp686H04208 (from clone DKFZp686H04208).
BX647568 - Homo sapiens mRNA; cDNA DKFZp313C0811 (from clone DKFZp313C0811).
AF118094 - Homo sapiens PRO2134 mRNA, complete cds.
BC021972 - Homo sapiens TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa, mRNA (cDNA clone MGC:15243 IMAGE:3935882), complete cds.
JD279911 - Sequence 260935 from Patent EP1572962.
JD313943 - Sequence 294967 from Patent EP1572962.
JD530437 - Sequence 511461 from Patent EP1572962.
JD166332 - Sequence 147356 from Patent EP1572962.
AK302226 - Homo sapiens cDNA FLJ50289 complete cds, highly similar to Transcription initiation factor TFIID subunit 11.
JD159963 - Sequence 140987 from Patent EP1572962.
JD213580 - Sequence 194604 from Patent EP1572962.
JD227923 - Sequence 208947 from Patent EP1572962.
JD342089 - Sequence 323113 from Patent EP1572962.
JD293456 - Sequence 274480 from Patent EP1572962.
JD051471 - Sequence 32495 from Patent EP1572962.
JD426030 - Sequence 407054 from Patent EP1572962.
JD480843 - Sequence 461867 from Patent EP1572962.
JD308310 - Sequence 289334 from Patent EP1572962.
JD435525 - Sequence 416549 from Patent EP1572962.
JD377450 - Sequence 358474 from Patent EP1572962.
JD454907 - Sequence 435931 from Patent EP1572962.
JD187444 - Sequence 168468 from Patent EP1572962.
JD146238 - Sequence 127262 from Patent EP1572962.
JD146796 - Sequence 127820 from Patent EP1572962.
JD417977 - Sequence 399001 from Patent EP1572962.
JD465131 - Sequence 446155 from Patent EP1572962.
JD271860 - Sequence 252884 from Patent EP1572962.
JD531399 - Sequence 512423 from Patent EP1572962.
JD501638 - Sequence 482662 from Patent EP1572962.
X83928 - H.sapiens mRNA for transcription factor TFIID subunit TAFII28.
JD524279 - Sequence 505303 from Patent EP1572962.
D63705 - Homo sapiens mRNA for TFIID subunit p30beta, complete cds.
JD286206 - Sequence 267230 from Patent EP1572962.
BT019404 - Homo sapiens TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa mRNA, complete cds.
BT019405 - Homo sapiens TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa mRNA, complete cds.
DQ893239 - Synthetic construct clone IMAGE:100005869; FLH195516.01X; RZPDo839D04152D TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa (TAF11) gene, encodes complete protein.
AK313475 - Homo sapiens cDNA, FLJ94022, Homo sapiens TAF11 RNA polymerase II, TATA box binding protein(TBP)-associated factor, 28kDa (TAF11), mRNA.
DQ896569 - Synthetic construct Homo sapiens clone IMAGE:100011029; FLH195512.01L; RZPDo839D04151D TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa (TAF11) gene, encodes complete protein.
AB464280 - Synthetic construct DNA, clone: pF1KB7569, Homo sapiens TAF11 gene for TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa, without stop codon, in Flexi system.
CR542068 - Homo sapiens full open reading frame cDNA clone RZPDo834G0636D for gene TAF11, TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa; complete cds, without stopcodon.
LF340907 - JP 2014500723-A/148410: Polycomb-Associated Non-Coding RNAs.
LF340908 - JP 2014500723-A/148411: Polycomb-Associated Non-Coding RNAs.
JD139393 - Sequence 120417 from Patent EP1572962.
JD255588 - Sequence 236612 from Patent EP1572962.
MA446341 - JP 2018138019-A/18267: Polycomb-Associated Non-Coding RNAs.
MA576484 - JP 2018138019-A/148410: Polycomb-Associated Non-Coding RNAs.
MA576485 - JP 2018138019-A/148411: Polycomb-Associated Non-Coding RNAs.

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

Reactome (by CSHL, EBI, and GO)

Protein Q15544 (Reactome details) participates in the following event(s):

R-HSA-109636 Recognition and Binding of Core Promoter Elements by TFIID
R-HSA-73946 Abortive initiation
R-HSA-75856 Abortive Initiation Before Second Transition
R-HSA-75873 Addition of Nucleotides 5 through 9 on the growing Transcript
R-HSA-167136 Addition of nucleotides 5 through 9 on the growing HIV-1 transcript
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-6810234 General transcription factors bind SNAPc:POU2F1:ZNF143:snRNA gene
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-109637 Binding of TFIIA and TFIIB to the pol II promoter:TFIID 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-6805399 TAF1 phosphorylates TP53
R-HSA-6810238 RNA polymerase II binds initiation factors at promoter of snRNA gene (U1, U2, U4, U4atac, U5, U11, U12)
R-HSA-109638 Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB 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-75095 Binding of TFIIE to the growing preinitiation complex
R-HSA-109639 Formation of the closed pre-initiation complex
R-HSA-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
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-6807505 RNA polymerase II transcribes snRNA genes
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-6804756 Regulation of TP53 Activity through Phosphorylation
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-74160 Gene expression (Transcription)
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-162587 HIV Life Cycle
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-162906 HIV Infection
R-HSA-212436 Generic Transcription Pathway
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B2R8R3, NM_005643, NP_005634, PRO2134, Q15544, Q9UHS0, TAF11_HUMAN, TAF2I, uc003ojw.1
UCSC ID: uc003ojw.2
RefSeq Accession: NM_005643
Protein: Q15544 (aka TAF11_HUMAN or TAFB_HUMAN)
CCDS: CCDS4797.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005643.3
exon count: 5CDS single in 3' UTR: no RNA size: 1587
ORF size: 636CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1457.00frame shift in genome: no % Coverage: 98.42
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.