Human Gene TFEB (uc003oqu.2)
  Description: Homo sapiens transcription factor EB (TFEB), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:41,651,716-41,703,997 Size: 52,282 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr6:41,652,337-41,703,903 Size: 51,567 Coding Exon Count: 9 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:41,651,716-41,703,997)mRNA (may differ from genome)Protein (490 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: B0QYS6_HUMAN
DESCRIPTION: SubName: Full=Transcription factor EB;
SIMILARITY: Contains 1 basic helix-loop-helix (bHLH) domain.

-  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): TFEB
CDC HuGE Published Literature: TFEB
Positive Disease Associations: ADHD | attention-deficit hyperactivity disorder , Coronary Disease , Metabolism
Related Studies:
  1. ADHD | attention-deficit hyperactivity disorder
    Lesch ,et al. 2008, Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies, Journal of neural transmission (Vienna, Austria : 1996) 2008 115- 11 : 1573-85. [PubMed 18839057]
  2. Coronary Disease
    , , . [PubMed 0]
  3. Metabolism
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TFEB
Diseases sorted by gene-association score: renal cell carcinoma, papillary* (159), microphthalmia (4), renal cell carcinoma (3), hemophagocytic lymphohistiocytosis, familial, 3 (2), childhood kidney cell carcinoma (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C547126 AZM551248
  • D016718 Arachidonic Acid
  • D012643 Selenium
  • D013749 Tetrachlorodibenzodioxin
  • D014118 Toxins, Biological
  • D014810 Vitamin E
  • C028007 nickel monoxide
  • C017947 sodium arsenite
          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: 24.61 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 297.90 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 -22.0094-0.234 Picture PostScript Text
3' UTR -314.00621-0.506 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
IPR024097 - bHLH_ZIP_TF
IPR021802 - bHLH_ZIP_TF_MiT/TFE
IPR011598 - HLH_dom
IPR024098 - TFEB

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF11851 - Domain of unknown function (DUF3371)
PF15951 - MITF/TFEB/TFEC/TFE3 N-terminus

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on B0QYS6
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0046983 protein dimerization activity

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0006959 humoral immune response
GO:0045893 positive regulation of transcription, DNA-templated


-  Descriptions from all associated GenBank mRNAs
  BC032448 - Homo sapiens transcription factor EB, mRNA (cDNA clone MGC:40490 IMAGE:5180066), complete cds.
AJ608786 - Homo sapiens mRNA for transcription factor EB (TFEB gene), splice variant A.
AK298390 - Homo sapiens cDNA FLJ55171 complete cds, highly similar to Transcription factor EB.
M33782 - Human TFEB protein mRNA, partial cds.
AK095061 - Homo sapiens cDNA FLJ37742 fis, clone BRHIP2022054, highly similar to Transcription factor EB.
AK310063 - Homo sapiens cDNA, FLJ17105.
AJ608790 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant 1e/1c2 including exon 1e.
AJ608791 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant including exon 1f.
AJ608787 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant C1.
AJ608789 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant including exon 1e.
AJ608788 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant including exon 1d.
BC006225 - Homo sapiens transcription factor EB, mRNA (cDNA clone IMAGE:3944945), partial cds.
JD137722 - Sequence 118746 from Patent EP1572962.
JD192404 - Sequence 173428 from Patent EP1572962.
JD141273 - Sequence 122297 from Patent EP1572962.
JD537714 - Sequence 518738 from Patent EP1572962.
JD222557 - Sequence 203581 from Patent EP1572962.
JD475162 - Sequence 456186 from Patent EP1572962.
JD195817 - Sequence 176841 from Patent EP1572962.
JD140028 - Sequence 121052 from Patent EP1572962.
JD483371 - Sequence 464395 from Patent EP1572962.
JD372866 - Sequence 353890 from Patent EP1572962.
JD526718 - Sequence 507742 from Patent EP1572962.
JD236055 - Sequence 217079 from Patent EP1572962.
JD455570 - Sequence 436594 from Patent EP1572962.
JD476262 - Sequence 457286 from Patent EP1572962.
JD540799 - Sequence 521823 from Patent EP1572962.
KJ892453 - Synthetic construct Homo sapiens clone ccsbBroadEn_01847 TFEB gene, encodes complete protein.
EU446667 - Synthetic construct Homo sapiens clone IMAGE:100070013; IMAGE:100011876; FLH258249.01L transcription factor EB (TFEB) gene, encodes complete protein.
AB527507 - Synthetic construct DNA, clone: pF1KB5822, Homo sapiens TFEB gene for transcription factor EB, without stop codon, in Flexi system.
CU689376 - Synthetic construct Homo sapiens gateway clone IMAGE:100019576 5' read TFEB mRNA.
AJ608794 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant 1g.
AJ608793 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant including exons 1g1 and 1g2.
AJ608792 - Homo sapiens partial mRNA for transcription factor EB (TFEB gene), splice variant including exon 1g1.

-  Other Names for This Gene
  Alternate Gene Symbols: B0QYS6, B0QYS6_HUMAN, NM_001167827, NP_001161299, RP4-696P19.3-010, uc003oqu.1
UCSC ID: uc003oqu.2
RefSeq Accession: NM_001167827
Protein: B0QYS6 CCDS: CCDS4858.1, CCDS64425.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001167827.2
exon count: 9CDS single in 3' UTR: no RNA size: 2280
ORF size: 1473CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3068.00frame shift in genome: no % Coverage: 95.96
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.