Human Gene TCF25 (uc010vpp.1) Description and Page Index
  Description: Homo sapiens transcription factor 25 (basic helix-loop-helix) (TCF25), mRNA.
RefSeq Summary (NM_014972): TCF25 is a member of the basic helix-loop-helix (bHLH) family of transcription factors that are important in embryonic development (Steen and Lindholm, 2008 [PubMed 18068114]).[supplied by OMIM, Sep 2008]. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.1091791.1, SRR1660809.32437.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000263346.13/ ENSP00000263346.8 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr16:89,939,994-89,950,471 Size: 10,478 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr16:89,940,076-89,949,932 Size: 9,857 Coding Exon Count: 2 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:89,939,994-89,950,471)mRNA (may differ from genome)Protein (121 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMGIPubMedStanford SOURCETreefam
UniProtKB

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TCF25
CDC HuGE Published Literature: TCF25

-  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: 58.81 RPKM in Pituitary
Total median expression: 2014.04 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 -21.7082-0.265 Picture PostScript Text
3' UTR -205.49539-0.381 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
IPR006994 - TCF25

ModBase Predicted Comparative 3D Structure on B4DVF2
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 orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK301053 - Homo sapiens cDNA FLJ59999 complete cds, highly similar to Transcription factor 25.
BC011884 - Homo sapiens transcription factor 25 (basic helix-loop-helix), mRNA (cDNA clone MGC:19865 IMAGE:3678670), complete cds.
JD139317 - Sequence 120341 from Patent EP1572962.
JD081846 - Sequence 62870 from Patent EP1572962.
JD235737 - Sequence 216761 from Patent EP1572962.
AF322111 - Homo sapiens FKSG26 mRNA, complete cds.
DQ321703 - Homo sapiens NULP1 (NULP1) mRNA, complete cds.
JD290814 - Sequence 271838 from Patent EP1572962.
AK024679 - Homo sapiens cDNA: FLJ21026 fis, clone CAE06812.
BC009349 - Homo sapiens transcription factor 25 (basic helix-loop-helix), mRNA (cDNA clone MGC:14951 IMAGE:4136178), complete cds.
BC000959 - Homo sapiens transcription factor 25 (basic helix-loop-helix), mRNA (cDNA clone MGC:5379 IMAGE:3445789), complete cds.
CU679309 - Synthetic construct Homo sapiens gateway clone IMAGE:100017450 5' read TCF25 mRNA.
CU674474 - Synthetic construct Homo sapiens gateway clone IMAGE:100020713 5' read TCF25 mRNA.
AB528245 - Synthetic construct DNA, clone: pF1KB6232, Homo sapiens TCF25 gene for transcription factor 25, without stop codon, in Flexi system.
AB587412 - Synthetic construct DNA, clone: pF1KB6232, Homo sapiens TCF25 gene for transcription factor 25, without stop codon, in Flexi system.
EU446609 - Synthetic construct Homo sapiens clone IMAGE:100069836; IMAGE:100011818; FLH258605.01L transcription factor 25 (basic helix-loop-helix) (TCF25) gene, encodes complete protein.
KJ906075 - Synthetic construct Homo sapiens clone ccsbBroadEn_15745 TCF25 gene, encodes complete protein.
KJ898430 - Synthetic construct Homo sapiens clone ccsbBroadEn_07824 TCF25 gene, encodes complete protein.
KJ904680 - Synthetic construct Homo sapiens clone ccsbBroadEn_14074 TCF25 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: AK301053, B4DVF2, B4DVF2_HUMAN
UCSC ID: uc010vpp.1
RefSeq Accession: NM_014972
Protein: B4DVF2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK301053.1
exon count: 2CDS single in 3' UTR: no RNA size: 981
ORF size: 366CDS single in intron: no Alignment % ID: 99.80
txCdsPredict score: 832.00frame shift in genome: no % Coverage: 100.00
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: 551# 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.