Human Gene TCF25 (ENST00000263346.13_6) from GENCODE V47lift37
  Description: transcription factor 25 (from RefSeq NM_014972.3)
Gencode Transcript: ENST00000263346.13_6
Gencode Gene: ENSG00000141002.20_11
Transcript (Including UTRs)
   Position: hg19 chr16:89,940,000-89,977,787 Size: 37,788 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr16:89,940,076-89,977,646 Size: 37,571 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:89,940,000-89,977,787)mRNA (may differ from genome)Protein (676 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TCF25_HUMAN
DESCRIPTION: RecName: Full=Transcription factor 25; Short=TCF-25; AltName: Full=Nuclear localized protein 1;
FUNCTION: May play a role in cell death control. Acts as a transcriptional repressor. Has been shown to repress transcription of SRF in vitro and so may play a role in heart development.
SUBUNIT: Interacts with XIAP (By similarity).
INTERACTION: P21673:SAT1; NbExp=3; IntAct=EBI-745182, EBI-711613;
SUBCELLULAR LOCATION: Nucleus. Note=Some staining in the cytosol.
TISSUE SPECIFICITY: In the embryo, widely expressed with highest levels in brain. In the adult, highest expression is found in the heart.
DOMAIN: The C-terminal region mediates transcriptional repression.
SIMILARITY: Belongs to the TCF25 family.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 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
  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 -19.0076-0.250 Picture PostScript Text
3' UTR -36.70141-0.260 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
IPR011990 - TPR-like_helical

Pfam Domains:
PF04910 - Transcriptional repressor TCF25

SCOP Domains:
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q9BQ70
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 BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007507 heart development

Cellular Component:
GO:0005634 nucleus


-  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.
AB028972 - Homo sapiens mRNA for KIAA1049 protein, partial cds.
AF130092 - Homo sapiens clone FLB9715 PRO2620 mRNA, complete cds.
DQ588015 - Homo sapiens piRNA piR-55127, complete sequence.
AK095785 - Homo sapiens cDNA FLJ38466 fis, clone FEBRA2021550, moderately similar to Mus musculus Nulp1 (nulp1) mRNA.
AK127949 - Homo sapiens cDNA FLJ46059 fis, clone TBAES2003435.
JD294952 - Sequence 275976 from Patent EP1572962.
JD170818 - Sequence 151842 from Patent EP1572962.
JD232606 - Sequence 213630 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000263346.1, ENST00000263346.10, ENST00000263346.11, ENST00000263346.12, ENST00000263346.2, ENST00000263346.3, ENST00000263346.4, ENST00000263346.5, ENST00000263346.6, ENST00000263346.7, ENST00000263346.8, ENST00000263346.9, FKSG26 , KIAA1049 , NM_014972, NULP1 , Q2MK75, Q9BQ70, Q9UPV3, TCF25 , TCF25_HUMAN, uc317hiw.1, uc317hiw.2
UCSC ID: ENST00000263346.13_6
RefSeq Accession: NM_014972.3
Protein: Q9BQ70 (aka TCF25_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.