Human Gene TAF9 (uc003jwc.1)
  Description: Homo sapiens TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa (TAF9), transcript variant 1, mRNA.
RefSeq Summary (NM_003187): 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 one of the smaller subunits of TFIID that binds to the basal transcription factor GTF2B as well as to several transcriptional activators such as p53 and VP16. In human, TAF9 and AK6 (GeneID: 102157402) are two distinct genes that share 5' exons. A similar but distinct gene (TAF9L) has been found on the X chromosome and a pseudogene has been identified on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013].
Transcript (Including UTRs)
   Position: hg19 chr5:68,660,570-68,662,644 Size: 2,075 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr5:68,660,770-68,661,564 Size: 795 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:68,660,570-68,662,644)mRNA (may differ from genome)Protein (264 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TAF9_HUMAN
DESCRIPTION: RecName: Full=Transcription initiation factor TFIID subunit 9; AltName: Full=RNA polymerase II TBP-associated factor subunit G; AltName: Full=STAF31/32; AltName: Full=Transcription initiation factor TFIID 31 kDa subunit; Short=TAFII-31; Short=TAFII31; AltName: Full=Transcription initiation factor TFIID 32 kDa subunit; Short=TAFII-32; Short=TAFII32;
FUNCTION: Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.
SUBUNIT: Component of TFIID, the TATA-binding protein-free TAF complex (TFTC), the PCAF complex and the STAGA transcription coactivator-HAT complex. The PCAF complex consists at least of TADA2L/ADA2, SUPT3H/SPT3, TADA3L/ADA3, TAF5L/PAF65-beta, TAF6L/PAF65-alpha, TAF10/TAFII30, TAF12/TAFII20, TAF9/TAFII31 and TRRAP. The STAGA transcription coactivator-HAT complex consists at least of SUPT3H, GCN5L2, SUPT7L, TAF5L, TAF6L, TADA3L, TAD1L, TAF10, TAF12, TRRAP and TAF9. Binds N-terminal domain of p53/TP53 which is essential for transcription. Component of some MLL1/MLL complex, at least composed of the core components MLL, ASH2L, HCFC1/HCF1, WDR5 and RBBP5, as well as the facultative components C17orf49, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, MYST1/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Binds TFIIB and the Herpes simplex virus activator VP16. Forms a heterodimer with TAF6/TAFII80 in a complex with the TAF4B/TAFII105-TAF12/TAFII20 heterodimer. Also interacts with TAF5. Binds directly DNA. Increased DNA binding when complexed with TAF6/TAFII80.
INTERACTION: Q92831:KAT2B; NbExp=3; IntAct=EBI-712521, EBI-477430; Q9Y6J9:TAF6L; NbExp=3; IntAct=EBI-712521, EBI-743984;
SUBCELLULAR LOCATION: Nucleus.
INDUCTION: 6 to 8-fold by apoptotic signals.
SIMILARITY: Belongs to the TAF9 family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/taf9/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TAF9
CDC HuGE Published Literature: TAF9

-  MalaCards Disease Associations
  MalaCards Gene Search: TAF9
Diseases sorted by gene-association score: spinocerebellar ataxia 7 (6)

-  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: 51.19 RPKM in Testis
Total median expression: 824.80 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 -83.95332-0.253 Picture PostScript Text
3' UTR -31.60200-0.158 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
IPR003162 - TFIID-31

Pfam Domains:
PF02291 - Transcription initiation factor IID, 31kD subunit

SCOP Domains:
47113 - Histone-fold

ModBase Predicted Comparative 3D Structure on Q16594
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002039 p53 binding
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0033613 activating transcription factor binding
GO:0044212 transcription regulatory region DNA binding
GO:0046982 protein heterodimerization activity
GO:0051117 ATPase binding
GO:0070742 C2H2 zinc finger domain binding
GO:0001075 transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly
GO:0004402 histone acetyltransferase activity

Biological Process:
GO:0000492 box C/D snoRNP assembly
GO:0006351 transcription, DNA-templated
GO:0006352 DNA-templated transcription, initiation
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:0006974 cellular response to DNA damage stimulus
GO:0030307 positive regulation of cell growth
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0042795 snRNA transcription from RNA polymerase II promoter
GO:0043066 negative regulation of apoptotic process
GO:0043966 histone H3 acetylation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0050821 protein stabilization
GO:0051123 RNA polymerase II transcriptional preinitiation complex assembly
GO:0060760 positive regulation of response to cytokine stimulus
GO:0070555 response to interleukin-1
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1902166 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

Cellular Component:
GO:0000124 SAGA complex
GO:0000125 PCAF complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005669 transcription factor TFIID complex
GO:0030914 STAGA complex
GO:0033276 transcription factor TFTC complex
GO:0070761 pre-snoRNP complex
GO:0071339 MLL1 complex


-  Descriptions from all associated GenBank mRNAs
  BC007349 - Homo sapiens TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, mRNA (cDNA clone MGC:1603 IMAGE:2966411), complete cds.
BC007426 - Homo sapiens TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, mRNA (cDNA clone MGC:3647 IMAGE:2966411), complete cds.
AF151895 - Homo sapiens CGI-137 protein mRNA, complete cds.
AF110777 - Homo sapiens adrenal gland protein AD-004 mRNA, complete cds.
AJ878880 - Homo sapiens mRNA for coilin-interacting nulcear ATPase protein (CINAP gene), from placenta.
AJ878881 - Homo sapiens mRNA for coilin-interacting nuclear ATPase protein (CINAP gene), clone library HeLa.
KJ905933 - Synthetic construct Homo sapiens clone ccsbBroadEn_15603 TAF9 gene, encodes complete protein.
EU831966 - Synthetic construct Homo sapiens clone HAIB:100066995; DKFZo008F0723 TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa protein (TAF9) gene, encodes complete protein.
EU832059 - Synthetic construct Homo sapiens clone HAIB:100067088; DKFZo004F0724 TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa protein (TAF9) gene, encodes complete protein.
U21858 - Human transcriptional activation factor TAFII32 mRNA, complete cds.
U25112 - Human TBP-associated factor TAFII31 mRNA, complete cds.
BC033320 - Homo sapiens TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, mRNA (cDNA clone MGC:42960 IMAGE:4837792), complete cds.
BC003400 - Homo sapiens TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa, mRNA (cDNA clone MGC:5067 IMAGE:3448836), complete cds.
U30504 - Human transcription initiation factor TFIID subunit TAFII31 mRNA, complete cds.
JD236662 - Sequence 217686 from Patent EP1572962.
BT019652 - Homo sapiens TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa mRNA, complete cds.
KJ892245 - Synthetic construct Homo sapiens clone ccsbBroadEn_01639 TAF9 gene, encodes complete protein.
AB464452 - Synthetic construct DNA, clone: pF1KB9673, Homo sapiens KAD6 gene for Adenylate kinase isoenzyme 6, without stop codon, in Flexi system.
JD020051 - Sequence 1075 from Patent EP1572962.
JD033849 - Sequence 14873 from Patent EP1572962.
CU678458 - Synthetic construct Homo sapiens gateway clone IMAGE:100018663 5' read TAF9 mRNA.
DQ571652 - Homo sapiens piRNA piR-31764, complete sequence.
LF365229 - JP 2014500723-A/172732: Polycomb-Associated Non-Coding RNAs.
LF365230 - JP 2014500723-A/172733: Polycomb-Associated Non-Coding RNAs.
JD514808 - Sequence 495832 from Patent EP1572962.
JD431771 - Sequence 412795 from Patent EP1572962.
MA600806 - JP 2018138019-A/172732: Polycomb-Associated Non-Coding RNAs.
MA600807 - JP 2018138019-A/172733: 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 Q16594 (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-3301237 KAT2 complexes acetylate histone H3
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-3214847 HATs acetylate histones
R-HSA-162587 HIV Life Cycle
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-162906 HIV Infection
R-HSA-212436 Generic Transcription Pathway
R-HSA-4839726 Chromatin organization
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: BC033320, D3DWA3, NM_003187, NP_003178, Q16594, Q5U0D1, Q9BTS1, TAF2G, TAF9_HUMAN, TAFII31
UCSC ID: uc003jwc.1
RefSeq Accession: NM_003187
Protein: Q16594 (aka TAF9_HUMAN)
CCDS: CCDS4002.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC033320.1
exon count: 2CDS single in 3' UTR: no RNA size: 2028
ORF size: 795CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 1775.00frame shift in genome: no % Coverage: 65.43
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: 222# 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.