Human Gene TFAM (ENST00000487519.6_4) from GENCODE V47lift37
  Description: transcription factor A, mitochondrial, transcript variant 3 (from RefSeq NR_073073.2)
Gencode Transcript: ENST00000487519.6_4
Gencode Gene: ENSG00000108064.11_8
Transcript (Including UTRs)
   Position: hg19 chr10:60,145,170-60,158,980 Size: 13,811 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr10:60,145,308-60,154,834 Size: 9,527 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:60,145,170-60,158,980)mRNA (may differ from genome)Protein (246 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TFAM_HUMAN
DESCRIPTION: RecName: Full=Transcription factor A, mitochondrial; Short=mtTFA; AltName: Full=Mitochondrial transcription factor 1; Short=MtTF1; AltName: Full=Transcription factor 6; Short=TCF-6; AltName: Full=Transcription factor 6-like 2; Flags: Precursor;
FUNCTION: Binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. Required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. Promotes transcription initiation from the HSP1 and the light strand promoter by binding immediately upstream of transcriptional start sites. Is able to unwind and bend DNA. Required for maintenance of normal levels of mitochondrial DNA. May play a role in organizing and compacting mitochondrial DNA. target DNA. Interacts with TFB1M and TFB2M. Associates with mitochondrial DNA.
INTERACTION: Q8WVM0:TFB1M; NbExp=2; IntAct=EBI-1049924, EBI-2615570;
SUBCELLULAR LOCATION: Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid.
SIMILARITY: Contains 2 HMG box DNA-binding domains.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: TFAM
Diseases sorted by gene-association score: mitochondrial dna depletion syndrome 15* (880), skin carcinoma in situ (15), extrahepatic cholestasis (12), mitochondrial disorders (7), autosomal dominant progressive external ophthalmoplegia (6), alzheimer disease mitochondrial (5), deafness, autosomal recessive 12 (4), myoclonic epilepsy associated with ragged-red fibers (3), dilated cardiomyopathy (2), kearns-sayre syndrome (1), parkinson disease, late-onset (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 17.06 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 236.77 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 -51.50138-0.373 Picture PostScript Text
3' UTR -1055.704146-0.255 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
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3FGH - X-ray MuPIT 3TMM - X-ray MuPIT 3TQ6 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q00059
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 orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001018 mitochondrial RNA polymerase regulatory region DNA binding
GO:0001223 transcription coactivator binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008301 DNA binding, bending
GO:0031072 heat shock protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006390 transcription from mitochondrial promoter
GO:0006391 transcription initiation from mitochondrial promoter
GO:0007005 mitochondrion organization
GO:0033108 mitochondrial respiratory chain complex assembly
GO:0045893 positive regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0032991 macromolecular complex
GO:0042645 mitochondrial nucleoid


-  Descriptions from all associated GenBank mRNAs
  BC029815 - Homo sapiens transcription factor A, mitochondrial, mRNA (cDNA clone IMAGE:5170491), with apparent retained intron.
AK312558 - Homo sapiens cDNA, FLJ92931, Homo sapiens transcription factor A, mitochondrial (TFAM), mRNA.
M62810 - Human mitochondrial transcription factor 1 mRNA, complete cds.
BC018628 - Homo sapiens transcription factor A, mitochondrial, mRNA (cDNA clone IMAGE:4552415), partial cds.
BC104482 - Homo sapiens transcription factor A, mitochondrial, mRNA (cDNA clone IMAGE:6717438), partial cds.
BC126366 - Homo sapiens transcription factor A, mitochondrial, mRNA (cDNA clone MGC:161644 IMAGE:8992082), complete cds.
JD544532 - Sequence 525556 from Patent EP1572962.
EU279428 - Homo sapiens mitochondrial transcription factor A (TFAM) mRNA, complete cds; nuclear gene for mitochondrial product.
HQ258758 - Synthetic construct Homo sapiens clone IMAGE:100072788 transcription factor A, mitochondrial (TFAM) gene, encodes complete protein; nuclear gene for mitochondrial product.
KJ897655 - Synthetic construct Homo sapiens clone ccsbBroadEn_07049 TFAM gene, encodes complete protein.
AB451366 - Homo sapiens TFAM mRNA for mitochondrial transcription factor A, partial cds, clone: FLJ08040AAAF.
AB464302 - Synthetic construct DNA, clone: pF1KB7516, Homo sapiens TFAM gene for mitochondrial transcription factor A, without stop codon, in Flexi system.
CR407653 - Homo sapiens full open reading frame cDNA clone RZPDo834H042D for gene TFAM, transcription factor A, mitochondrial complete cds, without stopcodon.
BT019658 - Homo sapiens transcription factor A, mitochondrial mRNA, complete cds.
BT019659 - Homo sapiens transcription factor A, mitochondrial mRNA, complete cds.
AB451241 - Homo sapiens TFAM mRNA for mitochondrial transcription factor A, complete cds, clone: FLJ08040AAAN.
JD434107 - Sequence 415131 from Patent EP1572962.
JD199394 - Sequence 180418 from Patent EP1572962.
JD549190 - Sequence 530214 from Patent EP1572962.
JD510453 - Sequence 491477 from Patent EP1572962.
JD433870 - Sequence 414894 from Patent EP1572962.
JD274015 - Sequence 255039 from Patent EP1572962.
JD233565 - Sequence 214589 from Patent EP1572962.

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

Protein Q00059 (Reactome details) participates in the following event(s):

R-HSA-163310 TFAM binds to mitochondrial promoters
R-HSA-163296 Association of TFAM:mt promoter complex with POLRMT:TFB2M
R-HSA-163282 Mitochondrial transcription initiation
R-HSA-2151201 Transcriptional activation of mitochondrial biogenesis
R-HSA-75944 Transcription from mitochondrial promoters
R-HSA-1592230 Mitochondrial biogenesis
R-HSA-74160 Gene expression (Transcription)
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: A8MRB2, A9QXC6, B5BU05, ENST00000487519.1, ENST00000487519.2, ENST00000487519.3, ENST00000487519.4, ENST00000487519.5, NR_073073, Q00059, Q5U0C6, TCF6, TCF6L2, TFAM , TFAM_HUMAN, uc322hsx.1, uc322hsx.2
UCSC ID: ENST00000487519.6_4
RefSeq Accession: NM_003201.3
Protein: Q00059 (aka TFAM_HUMAN)

-  Gene Model Information
  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.