Human Gene TAF1 (uc004dzt.4) Description and Page Index
  Description: Homo sapiens TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa (TAF1), transcript variant 1, mRNA.
RefSeq Summary (NM_004606): Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is the basal transcription factor 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 the largest subunit of TFIID. This subunit binds to core promoter sequences encompassing the transcription start site. It also binds to activators and other transcriptional regulators, and these interactions affect the rate of transcription initiation. This subunit contains two independent protein kinase domains at the N- and C-terminals, but also possesses acetyltransferase activity and can act as a ubiquitin-activating/conjugating enzyme. Mutations in this gene result in Dystonia 3, torsion, X-linked, a dystonia-parkinsonism disorder. Alternative splicing of this gene results in multiple transcript variants. This gene is part of a complex transcription unit (TAF1/DYT3), wherein some transcript variants share exons with TAF1 as well as additional downstream DYT3 exons. [provided by RefSeq, Oct 2013].
Transcript (Including UTRs)
   Position: hg19 chrX:70,586,114-70,685,855 Size: 99,742 Total Exon Count: 38 Strand: +
Coding Region
   Position: hg19 chrX:70,586,165-70,683,896 Size: 97,732 Coding Exon Count: 38 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:70,586,114-70,685,855)mRNA (may differ from genome)Protein (1893 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TAF1
CDC HuGE Published Literature: TAF1
Positive Disease Associations: angina , atherosclerosis, coronary , Atherothrombosis , blood pressure , meningococcal disease , microangiopathy, thrombotic , Thrombin activatable fibrinolysis inhibitor
Related Studies:
  1. angina
    Brouwers, G. J. et al. 2003, Association between thrombin-activatable fibrinolysis inhibitor (TAFI) and clinical outcome in patients with unstable angina pectoris., Thrombosis and haemostasis. 2003 Jul;90(1):92-100. [PubMed 12876631]
    In conclusion, in this study population plasma TAFI Ag levels are significantly correlated with refractiveness in patients with UAP. Furthermore, all three polymorphisms contribute independently to plasma TAFI Ag levels, but not to refractiveness.
  2. atherosclerosis, coronary
    Segev, A. et al. 2004, Thr325Ile polymorphism of the TAFI gene is related to TAFI antigen plasma levels and angiographic restenosis after percutaneous coronary interventions., Thrombosis research. 2004 ;114(2):137-41. [PubMed 15306156]
    These data suggest that plasma TAFI antigen levels are genetically controlled. The T/T Thr325Ile polymorphism of the TAFI gene is associated with lower plasma levels of TAFI antigen and lower restenosis rates after PCI.
  3. Atherothrombosis
    Morange PE 2003, , Thrombosis and haemostasis. 2003 Mar;89(3):554-60. [PubMed 12624641]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TAF1
Diseases sorted by gene-association score: dystonia-parkinsonism, x-linked* (1369), mental retardation, x-linked, syndromic 33* (1331), x-linked dystonia-parkinsonism/lubag* (400), dystonia (19), dystonia-1, torsion (8), dystonia, dopa-responsive, with or without hyperphenylalaninemia (7), hemidystonia (7), retinoblastoma (7), focal dystonia (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D004317 Doxorubicin
  • C016403 2,4-dinitrotoluene
  • C023514 2,6-dinitrotoluene
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • C017906 3-dinitrobenzene
  • C513003 5-(4-((6-(allyloxy)-2,5,7,8-tetramethylchroman-2-yl)methoxy)-3-methoxybenzylidene)thiazolidine-2,4-dione
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D004390 Chlorpyrifos
  • D002794 Choline
  • D003993 Dibutyl Phthalate
          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: 8.26 RPKM in Ovary
Total median expression: 264.78 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 -12.3051-0.241 Picture PostScript Text
3' UTR -583.911959-0.298 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
  Pfam Domains:
PF00439 - Bromodomain
PF09247 - TATA box-binding protein binding
PF12157 - Protein of unknown function (DUF3591)
PF15288 - Zinc knuckle

SCOP Domains:
47055 - TAF(II)230 TBP-binding fragment
47370 - Bromodomain

ModBase Predicted Comparative 3D Structure on P21675-2
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 BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  D90359 - Homo sapiens ccg1 mRNA for DNA binding protein, complete cds.
AB300418 - Homo sapiens N-TAF1 mRNA for TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, neuron specific isoform, complete cds.
BC172427 - Synthetic construct Homo sapiens clone IMAGE:100069121, MGC:199132 TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa (TAF1) mRNA, encodes complete protein.
AB209316 - Homo sapiens mRNA for TBP-associated factor 1 isoform 2 variant protein.
AM711892 - Homo sapiens partial mRNA for dystonia 3 (with Parkinsonism) (DYT3 gene).
AM711893 - Homo sapiens partial mRNA for dystonia 3 (with Parkinsonism) (DYT3 gene).
AM711894 - Homo sapiens partial mRNA for dystonia 3 (with Parkinsonism) (DYT3 gene).
AM711895 - Homo sapiens partial mRNA for dystonia 3 (with Parkinsonism) (DYT3 gene).
AJ549248 - Homo sapiens partial mRNA for putative DYT3 protein, splice variant 2a.
AJ549250 - Homo sapiens partial mRNA for putative DYT3 protein, splice variant 2c.
AJ555148 - Homo sapiens partial mRNA for putative DYT3 protein, splice variant 2d.
AJ555149 - Homo sapiens partial mRNA for putative DYT3 protein, splice variant 2e.
AJ549249 - Homo sapiens partial mRNA for putative DYT3 protein, splice variant 2b.
M73444 - Human CCG1p mRNA, 5' flank.
AK310201 - Homo sapiens cDNA, FLJ17243.
LF381748 - JP 2014500723-A/189251: Polycomb-Associated Non-Coding RNAs.
X07024 - Homo sapiens mRNA for CCG1 protein.
LF381749 - JP 2014500723-A/189252: Polycomb-Associated Non-Coding RNAs.
LF381750 - JP 2014500723-A/189253: Polycomb-Associated Non-Coding RNAs.
LF381752 - JP 2014500723-A/189255: Polycomb-Associated Non-Coding RNAs.
LF381754 - JP 2014500723-A/189257: Polycomb-Associated Non-Coding RNAs.
LF381755 - JP 2014500723-A/189258: Polycomb-Associated Non-Coding RNAs.
LF381756 - JP 2014500723-A/189259: Polycomb-Associated Non-Coding RNAs.
LF381757 - JP 2014500723-A/189260: Polycomb-Associated Non-Coding RNAs.
LF381759 - JP 2014500723-A/189262: Polycomb-Associated Non-Coding RNAs.
LF381760 - JP 2014500723-A/189263: Polycomb-Associated Non-Coding RNAs.
LF381761 - JP 2014500723-A/189264: Polycomb-Associated Non-Coding RNAs.
LF381762 - JP 2014500723-A/189265: Polycomb-Associated Non-Coding RNAs.
LF381763 - JP 2014500723-A/189266: Polycomb-Associated Non-Coding RNAs.
LF381764 - JP 2014500723-A/189267: Polycomb-Associated Non-Coding RNAs.
LF381765 - JP 2014500723-A/189268: Polycomb-Associated Non-Coding RNAs.
LF381766 - JP 2014500723-A/189269: Polycomb-Associated Non-Coding RNAs.
LF381767 - JP 2014500723-A/189270: Polycomb-Associated Non-Coding RNAs.
LF381768 - JP 2014500723-A/189271: Polycomb-Associated Non-Coding RNAs.
LF381769 - JP 2014500723-A/189272: Polycomb-Associated Non-Coding RNAs.
LF381771 - JP 2014500723-A/189274: Polycomb-Associated Non-Coding RNAs.
LF381772 - JP 2014500723-A/189275: Polycomb-Associated Non-Coding RNAs.
LF381773 - JP 2014500723-A/189276: Polycomb-Associated Non-Coding RNAs.
LF381774 - JP 2014500723-A/189277: Polycomb-Associated Non-Coding RNAs.
LF381775 - JP 2014500723-A/189278: Polycomb-Associated Non-Coding RNAs.
LF381779 - JP 2014500723-A/189282: Polycomb-Associated Non-Coding RNAs.
MA617325 - JP 2018138019-A/189251: Polycomb-Associated Non-Coding RNAs.
MA617326 - JP 2018138019-A/189252: Polycomb-Associated Non-Coding RNAs.
MA617327 - JP 2018138019-A/189253: Polycomb-Associated Non-Coding RNAs.
MA617329 - JP 2018138019-A/189255: Polycomb-Associated Non-Coding RNAs.
MA617331 - JP 2018138019-A/189257: Polycomb-Associated Non-Coding RNAs.
MA617332 - JP 2018138019-A/189258: Polycomb-Associated Non-Coding RNAs.
MA617333 - JP 2018138019-A/189259: Polycomb-Associated Non-Coding RNAs.
MA617334 - JP 2018138019-A/189260: Polycomb-Associated Non-Coding RNAs.
MA617336 - JP 2018138019-A/189262: Polycomb-Associated Non-Coding RNAs.
MA617337 - JP 2018138019-A/189263: Polycomb-Associated Non-Coding RNAs.
MA617338 - JP 2018138019-A/189264: Polycomb-Associated Non-Coding RNAs.
MA617339 - JP 2018138019-A/189265: Polycomb-Associated Non-Coding RNAs.
MA617340 - JP 2018138019-A/189266: Polycomb-Associated Non-Coding RNAs.
MA617341 - JP 2018138019-A/189267: Polycomb-Associated Non-Coding RNAs.
MA617342 - JP 2018138019-A/189268: Polycomb-Associated Non-Coding RNAs.
MA617343 - JP 2018138019-A/189269: Polycomb-Associated Non-Coding RNAs.
MA617344 - JP 2018138019-A/189270: Polycomb-Associated Non-Coding RNAs.
MA617345 - JP 2018138019-A/189271: Polycomb-Associated Non-Coding RNAs.
MA617346 - JP 2018138019-A/189272: Polycomb-Associated Non-Coding RNAs.
MA617348 - JP 2018138019-A/189274: Polycomb-Associated Non-Coding RNAs.
MA617349 - JP 2018138019-A/189275: Polycomb-Associated Non-Coding RNAs.
MA617350 - JP 2018138019-A/189276: Polycomb-Associated Non-Coding RNAs.
MA617351 - JP 2018138019-A/189277: Polycomb-Associated Non-Coding RNAs.
MA617352 - JP 2018138019-A/189278: Polycomb-Associated Non-Coding RNAs.
MA617356 - JP 2018138019-A/189282: Polycomb-Associated Non-Coding RNAs.
LF381783 - JP 2014500723-A/189286: Polycomb-Associated Non-Coding RNAs.
LF381786 - JP 2014500723-A/189289: Polycomb-Associated Non-Coding RNAs.
AJ549247 - Homo sapiens partial mRNA for putative DYT3 protein, splice variant 1.
LF381787 - JP 2014500723-A/189290: Polycomb-Associated Non-Coding RNAs.
LF381792 - JP 2014500723-A/189295: Polycomb-Associated Non-Coding RNAs.
JD365310 - Sequence 346334 from Patent EP1572962.
JD487148 - Sequence 468172 from Patent EP1572962.
JD492556 - Sequence 473580 from Patent EP1572962.
JD514291 - Sequence 495315 from Patent EP1572962.
JD071378 - Sequence 52402 from Patent EP1572962.
JD195354 - Sequence 176378 from Patent EP1572962.
JD163788 - Sequence 144812 from Patent EP1572962.
JD459605 - Sequence 440629 from Patent EP1572962.
JD168182 - Sequence 149206 from Patent EP1572962.
JD379101 - Sequence 360125 from Patent EP1572962.
JD403691 - Sequence 384715 from Patent EP1572962.
JD112328 - Sequence 93352 from Patent EP1572962.
JD294137 - Sequence 275161 from Patent EP1572962.
JD514945 - Sequence 495969 from Patent EP1572962.
JD421512 - Sequence 402536 from Patent EP1572962.
JD179116 - Sequence 160140 from Patent EP1572962.
JD361338 - Sequence 342362 from Patent EP1572962.
JD486708 - Sequence 467732 from Patent EP1572962.
JD266304 - Sequence 247328 from Patent EP1572962.
LF381793 - JP 2014500723-A/189296: Polycomb-Associated Non-Coding RNAs.
MA617360 - JP 2018138019-A/189286: Polycomb-Associated Non-Coding RNAs.
MA617363 - JP 2018138019-A/189289: Polycomb-Associated Non-Coding RNAs.
MA617364 - JP 2018138019-A/189290: Polycomb-Associated Non-Coding RNAs.
MA617369 - JP 2018138019-A/189295: Polycomb-Associated Non-Coding RNAs.
MA617370 - JP 2018138019-A/189296: Polycomb-Associated Non-Coding RNAs.

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

BioCarta from NCI Cancer Genome Anatomy Project
h_p53hypoxiaPathway - Hypoxia and p53 in the Cardiovascular system

Reactome (by CSHL, EBI, and GO)

Protein P21675 (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-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-109638 Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex
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-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: BA2R, CCG1, CCGS, NM_004606, NP_004597, P21675-2, TAF2A
UCSC ID: uc004dzt.4
RefSeq Accession: NM_004606
Protein: P21675-2, splice isoform of P21675 CCDS: CCDS14412.1, CCDS35325.1, CCDS69783.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TAF1:
dystonia-ov (Hereditary Dystonia Overview)
xdp (X-Linked Dystonia-Parkinsonism Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004606.3
exon count: 38CDS single in 3' UTR: no RNA size: 7709
ORF size: 5682CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9549.00frame shift in genome: no % Coverage: 99.78
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
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.