TCF25 Gene (Protein Coding)

Transcription Factor 25

GC16P089873
GIFtS:
39
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] See more...

Aliases for TCF25 Gene

Aliases for TCF25 Gene

  • Transcription Factor 25 2 3 4 5
  • Transcription Factor 25 (Basic Helix-Loop-Helix) 2 3
  • Nuclear Localized Protein 1 3 4
  • KIAA1049 2 4
  • TCF-25 3 4
  • NULP1 3 4
  • HKIAA1049 3
  • PRO2620 3
  • FKSG26 3
  • Hulp1 3
  • TCF25 5
  • Nulp1 2

External Ids for TCF25 Gene

Previous GeneCards Identifiers for TCF25 Gene

  • GC16P088469
  • GC16P089939
  • GC16P075633

Summaries for TCF25 Gene

Entrez Gene Summary for TCF25 Gene

  • 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]

GeneCards Summary for TCF25 Gene

TCF25 (Transcription Factor 25) is a Protein Coding gene. Diseases associated with TCF25 include Toe Syndactyly, Telecanthus, And Anogenital And Renal Malformations and Vulvovaginitis. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity.

UniProtKB/Swiss-Prot Summary for TCF25 Gene

  • 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.

Additional gene information for TCF25 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TCF25 Gene

Genomics for TCF25 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TCF25 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TCF25 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TCF25

Top Transcription factor binding sites by QIAGEN in the TCF25 gene promoter:
  • AP-1
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • ATF
  • GATA-2
  • Pax-2
  • Pax-2a
  • Pax-6

Genomic Locations for TCF25 Gene

Latest Assembly
chr16:89,873,570-89,913,627
(GRCh38/hg38)
Size:
40,058 bases
Orientation:
Plus strand

Previous Assembly
chr16:89,940,000-89,977,787
(GRCh37/hg19 by Entrez Gene)
Size:
37,788 bases
Orientation:
Plus strand

chr16:89,940,000-89,977,792
(GRCh37/hg19 by Ensembl)
Size:
37,793 bases
Orientation:
Plus strand

Genomic View for TCF25 Gene

Genes around TCF25 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TCF25 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TCF25 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TCF25 Gene

Proteins for TCF25 Gene

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  • Protein details for TCF25 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQ70-TCF25_HUMAN
    Recommended name:
    Transcription factor 25
    Protein Accession:
    Q9BQ70
    Secondary Accessions:
    • Q2MK75
    • Q9UPV3

    Protein attributes for TCF25 Gene

    Size:
    676 amino acids
    Molecular mass:
    76667 Da
    Quaternary structure:
    • Interacts with XIAP.

neXtProt entry for TCF25 Gene

Protein Expression for TCF25 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TCF25 Gene

  • Ubiquitination at Lys192 and Lys231
  • Modification sites at PhosphoSitePlus

Other Protein References for TCF25 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TCF25 Gene

Domains & Families for TCF25 Gene

Gene Families for TCF25 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TCF25 Gene

InterPro:
Blocks:
  • Protein of unknown function DUF654
ProtoNet:

Suggested Antigen Peptide Sequences for TCF25 Gene

GenScript: Design optimal peptide antigens:
  • cDNA: FLJ21026 fis, clone CAE06812 (Q9H7D3_HUMAN)
  • Nuclear localized protein 1 (TCF25_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BQ70

UniProtKB/Swiss-Prot:

TCF25_HUMAN :
  • The C-terminal region mediates transcriptional repression.
  • Belongs to the TCF25 family.
Domain:
  • The C-terminal region mediates transcriptional repression.
Family:
  • Belongs to the TCF25 family.
genes like me logo Genes that share domains with TCF25: view

Function for TCF25 Gene

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  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for TCF25 Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for TCF25 Gene

Gene Ontology (GO) - Molecular Function for TCF25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003714 transcription corepressor activity IDA 16574069
GO:0005515 protein binding IEA,IPI 16189514
genes like me logo Genes that share ontologies with TCF25: view
genes like me logo Genes that share phenotypes with TCF25: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TCF25

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TCF25 Gene

Localization for TCF25 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCF25 Gene

Nucleus. Note=Some staining in the cytosol.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TCF25 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for TCF25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 16574069
GO:1990112 RQC complex IBA 21873635
genes like me logo Genes that share ontologies with TCF25: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TCF25 Gene

Pathways & Interactions for TCF25 Gene

PathCards logo

SuperPathways for TCF25 Gene

genes like me logo Genes that share pathways with TCF25: view

Pathways by source for TCF25 Gene

1 Sino Biological pathway for TCF25 Gene

Gene Ontology (GO) - Biological Process for TCF25 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 16574069
GO:0007507 heart development NAS 16574069
genes like me logo Genes that share ontologies with TCF25: view

No data available for SIGNOR curated interactions for TCF25 Gene

Drugs & Compounds for TCF25 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for TCF25 Gene

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mRNA/cDNA for TCF25 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
26 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TCF25

Alternative Splicing Database (ASD) splice patterns (SP) for TCF25 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b · 14c · 14d ^ 15 ^ 16a · 16b ^ 17a ·
SP1: - - - - - -
SP2: - - - - -
SP3: - -
SP4: - -
SP5: - - - - - - - - - - - - -
SP6:
SP7:
SP8:
SP9:

ExUns: 17b ^ 18 ^ 19a · 19b ^ 20
SP1: - -
SP2: -
SP3:
SP4:
SP5:
SP6: - -
SP7:
SP8:
SP9:

Relevant External Links for TCF25 Gene

GeneLoc Exon Structure for
TCF25

Expression for TCF25 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TCF25 Gene

mRNA expression in normal human tissues for TCF25 Gene
mRNA expression by GTEx for TCF25 GenemRNA expression by BioGPS for TCF25 Gene

Protein differential expression in normal tissues from HIPED for TCF25 Gene

This gene is overexpressed in Breast (17.3) and Lung (10.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TCF25 Gene



Protein tissue co-expression partners for TCF25 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TCF25

SOURCE GeneReport for Unigene cluster for TCF25 Gene:

Hs.415342

mRNA Expression by UniProt/SwissProt for TCF25 Gene:

Q9BQ70-TCF25_HUMAN
Tissue specificity: In the embryo, widely expressed with highest levels in brain. In the adult, highest expression is found in the heart.

Evidence on tissue expression from TISSUES for TCF25 Gene

  • Nervous system(4.9)
  • Muscle(4.4)
  • Liver(4.4)
  • Lung(3.3)
  • Kidney(2.3)
  • Skin(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with TCF25: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TCF25 Gene

Orthologs for TCF25 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TCF25 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TCF25 30 31
  • 98.81 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TCF25 30 31
  • 87.08 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Tcf25 30
  • 86.83 (n)
Mouse
(Mus musculus)
 Mammalia Tcf25 30 17 31
  • 85.9 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TCF25 30 31
  • 83.9 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia TCF25 31
  • 65 (a)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TCF25 31
  • 61 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves TCF25 30 31
  • 68.38 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TCF25 31
  • 60 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia tcf25 30
  • 63.65 (n)
Str.8047 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.23789 30
Zebrafish
(Danio rerio)
 Actinopterygii tcf25 30 31
  • 60.88 (n)
 OneToOne
wufc09e07 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.5155 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP005545 30
  • 55.33 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta CG7927 30 31
  • 49.63 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea K07A12.1 31
  • 23 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes -- 31
  • 20 (a)
 OneToOne
RQC1 33
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT2G46900 30
  • 44.47 (n)
Rice
(Oryza sativa)
 Liliopsida Os09g0514900 30
  • 43.99 (n)
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC1142.01 30
  • 38.84 (n)
Species where no ortholog for TCF25 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TCF25 Gene

ENSEMBL:
Gene Tree for TCF25 (if available)
TreeFam:
Gene Tree for TCF25 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TCF25: view image

Paralogs for TCF25 Gene

(1) SIMAP similar genes for TCF25 Gene using alignment to 11 proteins:

  • TCF25_HUMAN
  • H3BMJ8_HUMAN
  • H3BPU1_HUMAN
  • H3BQ53_HUMAN
  • H3BR53_HUMAN
  • H3BRP4_HUMAN
  • H3BS87_HUMAN
  • H3BSP8_HUMAN
  • H3BSS3_HUMAN
  • H3BTU3_HUMAN
  • Q9H384_HUMAN
genes like me logo Genes that share paralogs with TCF25: view

No data available for Paralogs for TCF25 Gene

Variants for TCF25 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TCF25 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs139967795 Likely Benign: not provided 89,911,074(+) C/T
NM_014972.3(TCF25):c.1873-6C>T 		INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TCF25 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TCF25 Gene

Variant ID Type Subtype PubMed ID
dgv5336n54 CNV gain 21841781
dgv5337n54 CNV gain+loss 21841781
dgv5338n54 CNV gain+loss 21841781
dgv5339n54 CNV loss 21841781
dgv5340n54 CNV gain 21841781
dgv5341n54 CNV gain+loss 21841781
esv1230447 CNV deletion 17803354
esv1404867 CNV deletion 17803354
esv1411513 CNV deletion 17803354
esv1528431 CNV deletion 17803354
esv24531 CNV gain 19812545
esv2665192 CNV deletion 23128226
esv2758671 CNV loss 17122850
esv2762221 CNV gain+loss 21179565
esv3553918 CNV deletion 23714750
esv5359 CNV loss 18987735
nsv1066499 CNV loss 25217958
nsv1071318 CNV deletion 25765185
nsv1118366 CNV deletion 24896259
nsv428331 CNV gain+loss 18775914
nsv457624 CNV loss 19166990
nsv482951 CNV loss 15286789
nsv509640 CNV insertion 20534489
nsv511563 CNV loss 21212237
nsv512457 CNV loss 21212237
nsv526347 CNV loss 19592680
nsv573744 CNV loss 21841781
nsv573799 CNV gain 21841781
nsv573810 CNV loss 21841781
nsv573811 CNV gain+loss 21841781
nsv573812 CNV gain 21841781
nsv573813 CNV gain 21841781
nsv573816 CNV loss 21841781
nsv573825 CNV gain 21841781
nsv573839 CNV loss 21841781
nsv9479 CNV gain 18304495
nsv9481 CNV loss 18304495

Variation tolerance for TCF25 Gene

Residual Variation Intolerance Score: 33.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.78; 66.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TCF25 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TCF25

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCF25 Gene

Disorders for TCF25 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TCF25 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search TCF25 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TCF25

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TCF25: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TCF25 Gene

Publications for TCF25 Gene

  1. hnulp1, a basic helix-loop-helix protein with a novel transcriptional repressive domain, inhibits transcriptional activity of serum response factor. (PMID: 16574069) Cai Z … Wu X (Biochemical and biophysical research communications 2006) 2 3 4
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 41
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 41
  4. Nuclear localized protein-1 (Nulp1) increases cell death of human osteosarcoma cells and binds the X-linked inhibitor of apoptosis protein. (PMID: 18068114) Steen H … Lindholm D (Biochemical and biophysical research communications 2008) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

ExternalLinks

View latest publications for TCF25 gene in Mastermind

Products for TCF25 Gene

  • Addgene plasmids for TCF25

Sources for TCF25 Gene