Human Gene TAF1C (uc002fhm.3) Description and Page Index
  Description: Homo sapiens TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa (TAF1C), transcript variant 2, mRNA.
RefSeq Summary (NM_139353): Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs) specific for RNA polymerase I. This complex, known as SL1, binds to the core promoter of ribosomal RNA genes to position the polymerase properly and acts as a channel for regulatory signals. This gene encodes the largest SL1-specific TAF. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2011].
Transcript (Including UTRs)
   Position: hg19 chr16:84,211,453-84,220,676 Size: 9,224 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr16:84,212,547-84,217,321 Size: 4,775 Coding Exon Count: 13 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:84,211,453-84,220,676)mRNA (may differ from genome)Protein (775 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TAF1C
CDC HuGE Published Literature: TAF1C

-  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: 37.71 RPKM in Spleen
Total median expression: 857.98 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 -128.00282-0.454 Picture PostScript Text
3' UTR -419.901094-0.384 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
  ModBase Predicted Comparative 3D Structure on Q15572-2
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AB209594 - Homo sapiens mRNA for TBP-associated factor 1C isoform 1 variant protein.
AK304261 - Homo sapiens cDNA FLJ61071 complete cds, highly similar to TATA box-binding protein-associated factor RNA polymerase I subunit C.
L39059 - Homo sapiens transcription factor SL1 mRNA, complete cds.
BC028131 - Homo sapiens TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa, mRNA (cDNA clone MGC:39976 IMAGE:5205601), complete cds.
JD303058 - Sequence 284082 from Patent EP1572962.
JD508739 - Sequence 489763 from Patent EP1572962.
JD389669 - Sequence 370693 from Patent EP1572962.
JD526704 - Sequence 507728 from Patent EP1572962.
JD240122 - Sequence 221146 from Patent EP1572962.
JD405070 - Sequence 386094 from Patent EP1572962.
JD559782 - Sequence 540806 from Patent EP1572962.
JD496775 - Sequence 477799 from Patent EP1572962.
JD446158 - Sequence 427182 from Patent EP1572962.
JD493470 - Sequence 474494 from Patent EP1572962.
JD374015 - Sequence 355039 from Patent EP1572962.
JD459904 - Sequence 440928 from Patent EP1572962.
JD417099 - Sequence 398123 from Patent EP1572962.
JD035305 - Sequence 16329 from Patent EP1572962.
JD021227 - Sequence 2251 from Patent EP1572962.
JD027997 - Sequence 9021 from Patent EP1572962.
JD465921 - Sequence 446945 from Patent EP1572962.
JD536343 - Sequence 517367 from Patent EP1572962.
JD341965 - Sequence 322989 from Patent EP1572962.
JD361924 - Sequence 342948 from Patent EP1572962.
JD518889 - Sequence 499913 from Patent EP1572962.
JD530195 - Sequence 511219 from Patent EP1572962.
AK299347 - Homo sapiens cDNA FLJ61357 complete cds, highly similar to TATA box-binding protein-associated factor RNA polymerase I subunit C.
AK097031 - Homo sapiens cDNA FLJ39712 fis, clone SMINT2013129, highly similar to TATA box-binding protein-associated factor RNA polymerase I subunit C.
DQ594852 - Homo sapiens piRNA piR-60964, complete sequence.
AK299060 - Homo sapiens cDNA FLJ60815 complete cds, highly similar to TATA box-binding protein-associated factor RNA polymerase I subunit C.
JD151761 - Sequence 132785 from Patent EP1572962.
JD195319 - Sequence 176343 from Patent EP1572962.
AK315982 - Homo sapiens cDNA, FLJ78881 complete cds, highly similar to TATA box-binding protein-associated factor RNA polymerase I subunit C.
JD443194 - Sequence 424218 from Patent EP1572962.
JD065042 - Sequence 46066 from Patent EP1572962.
JD064179 - Sequence 45203 from Patent EP1572962.
JD386998 - Sequence 368022 from Patent EP1572962.
JD270988 - Sequence 252012 from Patent EP1572962.
JF432485 - Synthetic construct Homo sapiens clone IMAGE:100073706 TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa (TAF1C) gene, encodes complete protein.
KJ897942 - Synthetic construct Homo sapiens clone ccsbBroadEn_07336 TAF1C gene, encodes complete protein.
AB527611 - Synthetic construct DNA, clone: pF1KB0438, Homo sapiens TAF1C gene for TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa, without stop codon, in Flexi system.
AK304739 - Homo sapiens cDNA FLJ55276 complete cds, highly similar to TATA box-binding protein-associated factor RNA polymerase I subunit C.
JD054932 - Sequence 35956 from Patent EP1572962.
JD156905 - Sequence 137929 from Patent EP1572962.
JD265309 - Sequence 246333 from Patent EP1572962.
JD558637 - Sequence 539661 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q15572 (Reactome details) participates in the following event(s):

R-HSA-73729 Formation of SL1
R-HSA-73736 Acetylation of SL1
R-HSA-5250947 B-WICH complex binds rDNA promoter
R-HSA-5211239 SIRT1 deacetylates TAF1B in SL1 complex
R-HSA-73739 Recruitment of Acetylated SL1 to phosUBF-1:rDNA Promoter
R-HSA-5250930 B-WICH recruits histone acetyltransferases
R-HSA-73758 Recruitment of Active RNA Polymerase I to SL1:phos.UBF-1:rDNA Promoter
R-HSA-74994 Polymerase I Transcription Complex/Nascent Pre rRNA Complex pauses at the TTF-I:Sal Box
R-HSA-73769 Loss of Rrn3 from RNA Polymerase I promoter escape complex
R-HSA-74992 Dissociation of PTRF:Polymerase I/Nascent Pre rRNA Complex:TTF-I:Sal Box
R-HSA-74993 PTRF Binds the Polymerase I Transcription Complex/Nascent Pre rRNA Complex paused at the TTF-I:Sal Box
R-HSA-74986 Elongation of pre-rRNA transcript
R-HSA-427366 Transcription of intergenic spacer of the rRNA gene
R-HSA-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-427359 SIRT1 negatively regulates rRNA expression
R-HSA-73854 RNA Polymerase I Promoter Clearance
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-73863 RNA Polymerase I Transcription Termination
R-HSA-73772 RNA Polymerase I Promoter Escape
R-HSA-73864 RNA Polymerase I Transcription
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-73777 RNA Polymerase I Chain Elongation
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: NM_139353, NP_001230089, Q15572-2
UCSC ID: uc002fhm.3
RefSeq Accession: NM_139353
Protein: Q15572-2, splice isoform of Q15572 CCDS: CCDS45535.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_139353.2
exon count: 15CDS single in 3' UTR: no RNA size: 3720
ORF size: 2328CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 4564.00frame shift in genome: no % Coverage: 99.57
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.