Human Gene GTF3C6 (uc003pum.3) Description and Page Index
  Description: Homo sapiens general transcription factor IIIC, polypeptide 6, alpha 35kDa (GTF3C6), mRNA.
RefSeq Summary (NM_138408): RNA polymerases are unable to initiate RNA synthesis in the absence of additional proteins called general transcription factors (GTFs). GTFs assemble in a complex on the DNA promoter and recruit the RNA polymerase. GTF3C family proteins (e.g., GTF3C1, MIM 603246) are essential for RNA polymerase III to make a number of small nuclear and cytoplasmic RNAs, including 5S RNA (MIM 180420), tRNA, and adenovirus-associated (VA) RNA of both cellular and viral origin.[supplied by OMIM, Mar 2008]. ##Evidence-Data-START## Transcript exon combination :: AF361496.1, SRR1163657.272789.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000329970.8/ ENSP00000357863.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr6:111,279,763-111,289,091 Size: 9,329 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr6:111,279,973-111,288,993 Size: 9,021 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr6:111,279,763-111,289,091)mRNA (may differ from genome)Protein (213 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=General transcription factor 3C polypeptide 6; AltName: Full=Transcription factor IIIC 35 kDa subunit; Short=TFIIIC 35 kDa subunit; Short=TFIIIC35; AltName: Full=Transcription factor IIIC subunit 6;
FUNCTION: Involved in RNA polymerase III-mediated transcription. Integral, tightly associated component of the DNA-binding TFIIIC2 subcomplex that directly binds tRNA and virus-associated RNA promoters.
SUBUNIT: Part of the TFIIIC subcomplex TFIIIC2, consisting of six subunits, GTF3C1, GTF3C2, GTF3C3, GTF3C4, GTF3C5 and GTF3C6. Interacts with GTF3C4 and GTF3C5.
SIMILARITY: Belongs to the TFIIIC subunit 6 family.

-  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: 57.72 RPKM in Testis
Total median expression: 1413.86 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 -108.02210-0.514 Picture PostScript Text
3' UTR -11.3098-0.115 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
IPR019481 - TFIIIC_tau55-rel

Pfam Domains:
PF10419 - TFIIIC subunit

ModBase Predicted Comparative 3D Structure on Q969F1
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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006383 transcription from RNA polymerase III promoter
GO:0042791 5S class rRNA transcription from RNA polymerase III type 1 promoter
GO:0042797 tRNA transcription from RNA polymerase III promoter

Cellular Component:
GO:0000127 transcription factor TFIIIC complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016604 nuclear body

-  Descriptions from all associated GenBank mRNAs
  AF361496 - Homo sapiens NPD020 mRNA, complete cds.
AF361492 - Homo sapiens CDA020 mRNA, complete cds.
BC104655 - Homo sapiens general transcription factor IIIC, polypeptide 6, alpha 35kDa, mRNA (cDNA clone IMAGE:6739343), partial cds.
BC011593 - Homo sapiens general transcription factor IIIC, polypeptide 6, alpha 35kDa, mRNA (cDNA clone MGC:20479 IMAGE:4639268), complete cds.
AK057977 - Homo sapiens cDNA FLJ25248 fis, clone STM03469.
KJ899979 - Synthetic construct Homo sapiens clone ccsbBroadEn_09373 GTF3C6 gene, encodes complete protein.
EF137904 - Homo sapiens TFIIIC35 mRNA, complete cds.

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

Protein Q969F1 (Reactome details) participates in the following event(s):

R-HSA-76054 Binding of TFIIIC to TFIIIA:Type I Promoter complex
R-HSA-83788 Binding of TFIIIC to Type 2 promoter
R-HSA-83723 Binding of TFIIIB to TFIIIC:TFIIIA:Type I Promoter complex
R-HSA-83790 Binding of TFIIIB to TFIIC: Type 2 Promoter Complex
R-HSA-112055 RNA Polymerase III Abortive Initiation At Type 1 Open Promoters
R-HSA-112153 RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters
R-HSA-76060 RNA Polymerase III Promoter Opening at Type 1 Promoters
R-HSA-112149 RNA Polymerase III Abortive Initiation At Type 2 Open Promoters
R-HSA-112155 RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters
R-HSA-112150 RNA Polymerase III Promoter Opening at Type 2 Promoters
R-HSA-76056 Recruitment of RNA polymerase III to TFIIIB:TFIIIC:TFIIIA:Type 1 Promoter Complex
R-HSA-83805 Recruitment of RNA Polymerase III to the TFIIIB:TFIIIC: Type 2 Promoter Complex
R-HSA-76061 RNA Polymerase III Transcription Initiation From Type 1 Promoter
R-HSA-76066 RNA Polymerase III Transcription Initiation From Type 2 Promoter
R-HSA-749476 RNA Polymerase III Abortive And Retractive Initiation
R-HSA-76046 RNA Polymerase III Transcription Initiation
R-HSA-74158 RNA Polymerase III Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: C6orf51, CDA020, NM_138408, NPD020, NP_612417, Q5VXN2, Q969F1, TF3C6_HUMAN
UCSC ID: uc003pum.3
RefSeq Accession: NM_138408
Protein: Q969F1 (aka TF3C6_HUMAN)
CCDS: CCDS5087.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_138408.3
exon count: 6CDS single in 3' UTR: no RNA size: 957
ORF size: 642CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1451.00frame shift in genome: no % Coverage: 99.27
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.