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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TCF15 Gene

protein-coding   GIFtS: 48
GCID: GC20M000532

Transcription Factor 15 (Basic Helix-Loop-Helix)

  Search for TCF15
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Transcription Factor 15 (Basic Helix-Loop-Helix)1 2     PARAXIS2
Class A Basic Helix-Loop-Helix Protein 402 3     Basic Helix-Loop-Helix Transcription Factor 152
Protein BHLH-EC22 3     Transcription Factor 152
TCF-152 3     BHLHA403
bHLHa402 3     BHLHEC23
EC22     Paraxis3

External Ids:    HGNC: 116271   Entrez Gene: 69392   Ensembl: ENSG000001258787   OMIM: 6010105   UniProtKB: Q128703   
ORGUL members:         
NONCODE14:n339549      

Export aliases for TCF15 gene to outside databases

Previous GC identifers: GC20M000572 GC20M000579


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TCF15 Gene:
The protein encoded by this gene is found in the nucleus and may be involved in the early transcriptional
regulation of patterning of the mesoderm. The encoded basic helix-loop-helix protein requires dimerization with
another basic helix-loop-helix protein for efficient DNA binding. (provided by RefSeq, Jul 2008)

GeneCards Summary for TCF15 Gene: 
TCF15 (transcription factor 15 (basic helix-loop-helix)) is a protein-coding gene, and is affiliated with the lncRNA class. Among its related super-pathways are Factors Promoting Cardiogenesis in Vertebrates and MAPK Signaling. GO annotations related to this gene include protein dimerization activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is NHLH1.

UniProtKB/Swiss-Prot: TCF15_HUMAN, Q12870
Function: May function as an early transcriptional regulator, involved in the patterning of the mesoderm and in
lineage determination of cell types derived from the mesoderm




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.2  NT_011387.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TCF15 gene promoter:
         RORalpha1   E2F-1   FOXO4   p300   IRF-7A   MyoD   IRF-1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTCF15 promoter sequence
   Search SABiosciences Chromatin IP Primers for TCF15

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TCF15


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

TCF15 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TCF15 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M000532:  view genomic region     (about GC identifiers)

Start:
584,441 bp from pter      End:
591,042 bp from pter
Size:
6,602 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TCF15_HUMAN, Q12870 (See protein sequence)
Recommended Name: Transcription factor 15  
Size: 199 amino acids; 20816 Da
Subunit: Efficient DNA binding requires dimerization with another bHLH protein (By similarity)
Subcellular location: Nucleus (By similarity)
Secondary accessions: Q9NQQ1

Explore the universe of human proteins at neXtProt for TCF15: NX_Q12870

Explore proteomics data for TCF15 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q12870

  • TCF15 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    TCF15 Protein Expression
    REFSEQ proteins: NP_004600.2  
    ENSEMBL proteins: 
     ENSP00000246080  

    Human Recombinant Protein Products for TCF15: 
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    Cloud-Clone Corp. Proteins for TCF15 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    TCF15 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    bHLH: Basic helix-loop-helix proteins

    1 InterPro protein domain:
     IPR011598 bHLH_dom

    Graphical View of Domain Structure for InterPro Entry Q12870

    ProtoNet protein and cluster: Q12870

    1 Blocks protein domain: IPB001092 Basic helix-loop-helix dimerization domain bHLH

    UniProtKB/Swiss-Prot: TCF15_HUMAN, Q12870
    Similarity: Contains 1 bHLH (basic helix-loop-helix) domain


    TCF15 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TCF15_HUMAN, Q12870
    Function: May function as an early transcriptional regulator, involved in the patterning of the mesoderm and in
    lineage determination of cell types derived from the mesoderm

         Genatlas biochemistry entry for TCF15:
    transcription factor 15,expressed in early mesoderma and developing somites in the mouse embryo

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS8041747
    GO:0046983protein dimerization activity IEA--
         
    TCF15 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for TCF15:
     Decreased nuclei size in G2M 

         11 MGI mutant phenotypes (inferred from 1 allele(MGI details for Tcf15):
     behavior/neurological  craniofacial  embryogenesis  growth/size  hearing/vestibular/ear 
     integument  limbs/digits/tail  mortality/aging  muscle  respiratory system 
     skeleton 

    TCF15 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Tcf15tm1Eno for TCF15

       inGenious Targeting Laboratory - Custom generated mouse model solutions for TCF15 
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for TCF15 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Human Embryonic Stem Cell Pluripotency
    Human Embryonic Stem Cell Pluripotency0.50
    Factors Promoting Cardiogenesis in Vertebrates0.50
    2Rho Family GTPases
    MAPK Signaling0.58
    ILK Signaling0.49
    3TGF-Beta Pathway
    JNK Pathway0.51
    4PAK Pathway
    Epithelial Adherens Junctions0.36
    5WNT Signaling
    WNT Signaling

    5/7 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for TCF15 (see all 7)
        MAPK Signaling
    ILK Signaling
    Factors Promoting Cardiogenesis in Vertebrates
    Human Embryonic Stem Cell Pluripotency
    JNK Pathway


    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TCF15

    Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001756somitogenesis IEA--
    GO:0003016respiratory system process IEA--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006357regulation of transcription from RNA polymerase II promoter TAS8825648
    GO:0007498mesoderm development TAS8041747

    TCF15 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TCF15

    Search CenterWatch for drugs/clinical trials and news about TCF15

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TCF15 gene: 
    NM_004609.3  

    Unigene Cluster for TCF15:

    Transcription factor 15 (basic helix-loop-helix)
    Hs.437  [show with all ESTs]
    Unigene Representative Sequence: NM_004609
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000246080(uc002wdz.3)
    miRNA
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    hsa-miR-615-5p hsa-miR-1237 hsa-miR-4312 hsa-miR-342-3p hsa-miR-132 hsa-miR-3921 hsa-miR-766 hsa-miR-1248
    SwitchGear 3'UTR luciferase reporter plasmidTCF15 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: U08336.1 

    1 DOTS entry:

    DT.204030 

    21 AceView cDNA sequences:

    AI086393 AI218364 AA248660 AI377817 BM665510 AI452773 BV191902 BC067836 
    AI393227 AW290965 AI377586 AI699315 BV190930 NM_004609 AI452694 BF223969 
    BM711595 BG149324 AI183604 AI801955 U08336 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TCF15 expression in normal human tissues (normalized intensities)      TCF15 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCTGTTCCG
    TCF15 Expression
    About this image


    TCF15 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/4 selected tissues (see all 4) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 20 entries
             Muscle Progenitor Cells Sacral Ventrolateral Dermomyotome Lip
     
     Somite (Muscoskeletal System)    fully expand to see all 20 entries
             Muscle Progenitor Cells Sacral Ventrolateral Dermomyotome Lip
     
     Blood (Hematopoietic System)    fully expand to see all 3 entries
             reticulocytes   
     
     Umbilical Cord (Extraembryonic Tissues)
             umbilical cord reticulocytes   

    See TCF15 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TCF15

    SOURCE GeneReport for Unigene cluster: Hs.437
        SABiosciences Expression via Pathway-Focused PCR Array including TCF15: 
              Notch Signaling Targets in human mouse rat

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for TCF15 gene from 6/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tcf151 , 5 transcription factor 151, 5 92.31(n)1
    94.87(a)1
      2 (74.83 cM)5
    214071  NM_009328.21  NP_033354.21 
     1521435615 
    chicken
    (Gallus gallus)
    Aves TCF151 transcription factor 15 (basic helix-loop-helix) 79.78(n)
    78.14(a)
      395788  NM_204946.2  NP_990277.1 
    lizard
    (Anolis carolinensis)
    Reptilia TCF156
    Uncharacterized protein
    80(a)
    1 ↔ 1
    GL343346.1(169838-170308)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.159262 Xenopus laevis transcribed sequence with weak similarity more 78.81(n)    BJ029684.1 
    zebrafish
    (Danio rerio)
    Actinopterygii par12 paraxis 80.17(n)   30159  AJ006310.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG335576
    --
    39(a)
    1 → many
    X(9903268-9903886)


    ENSEMBL Gene Tree for TCF15 (if available)
    TreeFam Gene Tree for TCF15 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TCF15 gene
    NHLH12  TWIST12  HAND22  TWIST22  TAL12  NHLH22  LYL12  TAL22  
    SCXB2  HAND12  SCXA2  
    9 SIMAP similar genes for TCF15 using alignment to 3 protein entries:     TCF15_HUMAN (see all proteins):
    NHLH2    SCXA    SCXB    TAL2    TWIST2    ATOH7
    HAND2    TCF21    NHLH1

    TCF15 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/181 SNPs in TCF15 are shown (see all 181)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1513365811,2
    --584178(+) ACCCTA/GCCACG 1 -- ds50010--------
    rs1144455441,2
    C,F--584195(+) TGGGTG/ATCATC 1 -- ds50011Minor allele frequency- A:0.06WA 118
    rs1916316601,2
    --584350(+) AATAAG/TAAGCA 1 -- ds50010--------
    rs1816255251,2
    --584369(+) AGAAAC/TGAAAT 1 -- ds50010--------
    rs2012167141,2
    C--584424(+) GAAAA-/AAGAGAAG 1 -- ds50010--------
    rs1862479381,2
    C--584434(+) GGAGCC/TAAAAG 1 -- ds50010--------
    rs455149951,2
    C,F--584459(-) CACAAA/CTGACA 1 -- ds50011Minor allele frequency- C:0.01NS 158
    rs1902329831,2
    --584507(+) GGAAAC/TTGGTG 1 -- ds50010--------
    rs1428706951,2
    --584669(+) TTTACA/CAACCA 1 -- ut310--------
    rs1450405901,2
    --584731(+) AAAGTC/TTGGTT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for TCF15 (584441 - 591042 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for TCF15:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv4510n71CNV Loss21882294
    nsv912573CNV Loss21882294
    nsv458845CNV Loss19166990
    dgv4511n71CNV Loss21882294
    nsv458844CNV Loss19166990
    nsv912569CNV Loss21882294
    nsv469833CNV Gain16826518
    nsv828661CNV Gain20364138
    nsv833891CNV Gain+Loss17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    TCF15 for disorders           About MalaCards
    OMIM gene information: 601010    OMIM disorders: --


    TCF15 for disorders           About GeneDecksing


    Export disorders for TCF15 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for TCF15 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with TCF15)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of a basic helix-loop-helix protein expressed in early mesoderm and the developing somites. (PubMed id 8041747)1, 2, 3 Quertermous E.E....Quertermous T. (1994)
    2. Genomic organization and chromosomal localization of the gene TCF15 encoding the early mesodermal basic helix-loop-helix factor bHLH-EC2. (PubMed id 8825648)1, 3, 9 Hidai H....Quertermous T. (1995)
    3. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    4. A cohesin-RAD21 interactome. (PubMed id 22145905)1 Panigrahi A.K....Pati D. (2012)
    5. Acetylation of KLF5 alters the assembly of p15 transc ription factors in transforming growth factor-beta-mediated induction in epithe lial cells. (PubMed id 19419955)1 Guo P....Dong J.T. (2009)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    7. Xenopus paraxis homologue shows novel domains of expression. (PubMed id 15376281)9 Carpio R....Mayor R. (2004)
    8. Regulation of paraxis expression and somite formation by ectoderm- and neural tube-derived signals. (PubMed id 9187085)9 Sosic D....Olson E.N. (1997)
    9. Identification and developmental expression of Xenopus paraxis. (PubMed id 15602702)9 Tseng H.T. and Jamrich M. (2004)
    10. beta-Catenin-dependent Wnt signalling controls the epithelial organisation of somites through the activation of paraxis. (PubMed id 16100089)9 Linker C....Marcelle C. (2005)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6939 HGNC: 11627 AceView: TCF15 Ensembl:ENSG00000125878 euGenes: HUgn6939
    ECgene: TCF15 H-InvDB: TCF15

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for TCF15 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TCF15 gene:
    Search GeneIP for patents involving TCF15

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