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    TCF12 transcription factor 12 [ Homo sapiens (human) ]

    Gene ID: 6938, updated on 21-Apr-2019

    Summary

    Official Symbol
    TCF12provided by HGNC
    Official Full Name
    transcription factor 12provided by HGNC
    Primary source
    HGNC:HGNC:11623
    See related
    Ensembl:ENSG00000140262 MIM:600480
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HEB; p64; CRS3; HTF4; TCF-12; bHLHb20; HsT17266
    Summary
    The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 23.3), endometrium (RPKM 15.8) and 25 other tissues See more
    Orthologs

    Genomic context

    See TCF12 in Genome Data Viewer
    Location:
    15q21.3
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 15 NC_000015.10 (56918090..57292595)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (57210833..57580716)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene acyl-CoA binding domain containing 7 pseudogene Neighboring gene uncharacterized LOC105370833 Neighboring gene uncharacterized LOC145783 Neighboring gene VISTA enhancer hs357 Neighboring gene VISTA enhancer hs623 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 11 Neighboring gene small nucleolar RNA, C/D box 13D Neighboring gene long intergenic non-protein coding RNA 926 Neighboring gene long intergenic non-protein coding RNA 1413

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Craniosynostosis 3
    MedGen: C3715051 OMIM: 615314 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2015-10-15)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2015-10-15)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of transcription factor 12 (TCF12; HTF4) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr HIV-1 Vpr downregulates the gene expression of TCF12 in human monocyte-derived dendritic cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • CDO in myogenesis, organism-specific biosystem (from REACTOME)
      CDO in myogenesis, organism-specific biosystemCDO/Cdon (cell-adhesion-molecule-related/downregulated by oncogenes) is a type I transmembrane multifunctional co-receptor consisting of five immunoglobulin and three fibronectin type III (FNIII) rep...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • Myogenesis, organism-specific biosystem (from REACTOME)
      Myogenesis, organism-specific biosystemMyogenesis, the formation of muscle tissue, is a complex process involving steps of cell proliferation mediated by growth factor signaling, cell differentiation, reorganization of cells to form myotu...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    RNA polymerase II transcription factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor 12
    Names
    DNA-binding protein HTF4
    E-box-binding protein
    class B basic helix-loop-helix protein 20
    helix-loop-helix transcription factor 4
    transcription factor HTF-4

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_033851.2 RefSeqGene

      Range
      5546..375429
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001306219.2NP_001293148.1  transcription factor 12 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks multiple exon in the 5' UTR and 5' coding region and uses an alternate 5' most exon compared to variant 1. The encoded isoform (d) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC016525, AC090532
      Consensus CDS
      CCDS76760.1
      UniProtKB/TrEMBL
      F5GY10
      Related
      ENSP00000440017.1, ENST00000543579.5
      Conserved Domains (1) summary
      smart00353
      Location:437490
      HLH; helix loop helix domain
    2. NM_001306220.2NP_001293149.1  transcription factor 12 isoform e

      See identical proteins and their annotated locations for NP_001293149.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) has multiple differences in the 5' UTR and coding region compared to variant 1. The encoded isoform (e) is shorter and has a distict N-terminus compared to isoform a.
      Source sequence(s)
      AC016525, AC090532
      Consensus CDS
      CCDS76761.1
      UniProtKB/Swiss-Prot
      Q99081
      Related
      ENSP00000444696.1, ENST00000537840.5
      Conserved Domains (2) summary
      smart00353
      Location:347400
      HLH; helix loop helix domain
      pfam10428
      Location:13152
      SOG2; RAM signalling pathway protein
    3. NM_001322151.1NP_001309080.1  transcription factor 12 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Consensus CDS
      CCDS10160.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5Z0
      Conserved Domains (1) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
    4. NM_001322152.1NP_001309081.1  transcription factor 12 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Conserved Domains (2) summary
      smart00353
      Location:606659
      HLH; helix loop helix domain
      pfam09786
      Location:275448
      CytochromB561_N; Cytochrome B561, N terminal
    5. NM_001322154.1NP_001309083.1  transcription factor 12 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Conserved Domains (2) summary
      smart00353
      Location:388441
      HLH; helix loop helix domain
      pfam09786
      Location:56229
      CytochromB561_N; Cytochrome B561, N terminal
    6. NM_001322156.1NP_001309085.1  transcription factor 12 isoform h

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Conserved Domains (2) summary
      smart00353
      Location:549602
      HLH; helix loop helix domain
      pfam09786
      Location:217390
      CytochromB561_N; Cytochrome B561, N terminal
    7. NM_001322157.1NP_001309086.1  transcription factor 12 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Consensus CDS
      CCDS10159.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5T1
      Conserved Domains (1) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
    8. NM_001322158.1NP_001309087.1  transcription factor 12 isoform i

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Conserved Domains (1) summary
      smart00353
      Location:525578
      HLH; helix loop helix domain
    9. NM_001322159.1NP_001309088.1  transcription factor 12 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Consensus CDS
      CCDS10160.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5Z0
      Related
      ENSP00000453876.1, ENST00000559609.5
      Conserved Domains (1) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
    10. NM_001322161.1NP_001309090.1  transcription factor 12 isoform k

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Conserved Domains (2) summary
      smart00353
      Location:606659
      HLH; helix loop helix domain
      pfam09786
      Location:275447
      CytochromB561_N; Cytochrome B561, N terminal
    11. NM_001322162.1NP_001309091.1  transcription factor 12 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Consensus CDS
      CCDS10160.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5Z0
      Conserved Domains (1) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
    12. NM_001322164.1NP_001309093.1  transcription factor 12 isoform j

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Conserved Domains (1) summary
      smart00353
      Location:595648
      HLH; helix loop helix domain
    13. NM_001322165.1NP_001309094.1  transcription factor 12 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC010999, AC016525, AC090511, AC090532
      Consensus CDS
      CCDS10159.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5T1
      Conserved Domains (1) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
    14. NM_003205.3NP_003196.1  transcription factor 12 isoform b

      See identical proteins and their annotated locations for NP_003196.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding region (compared to variant 1), resulting in a protein that maintains the reading frame but is shorter, compared to isoform a. Variants 3 and 4 encode the same isoform b.
      Source sequence(s)
      AL831981, BC050556, BC051769, BK001049, BU178185, BX537967, M83233
      Consensus CDS
      CCDS10159.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5T1
      Related
      ENSP00000267811.5, ENST00000267811.9
      Conserved Domains (1) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
    15. NM_207036.1NP_996919.1  transcription factor 12 isoform a

      See identical proteins and their annotated locations for NP_996919.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform a.
      Source sequence(s)
      AL831981, BC050556, BK001049, BX537967
      Consensus CDS
      CCDS10160.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5Z0
      Related
      ENSP00000388940.2, ENST00000438423.6
      Conserved Domains (1) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
    16. NM_207037.1NP_996920.1  transcription factor 12 isoform a

      See identical proteins and their annotated locations for NP_996920.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform a.
      Source sequence(s)
      AL831981, BC050556, BK001049, BU178185, BX537967
      Consensus CDS
      CCDS10160.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5Z0
      Related
      ENSP00000331057.5, ENST00000333725.9
      Conserved Domains (1) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
    17. NM_207038.1NP_996921.1  transcription factor 12 isoform b

      See identical proteins and their annotated locations for NP_996921.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the coding region (compared to variant 1), resulting in a protein that maintains the reading frame but is shorter, compared to isoform a. Variants 3 and 4 encode the same isoform b.
      Source sequence(s)
      BC051769, BK001049, M80627
      Consensus CDS
      CCDS10159.1
      UniProtKB/Swiss-Prot
      Q99081
      UniProtKB/TrEMBL
      A0A024R5T1
      Related
      ENSP00000453737.1, ENST00000557843.5
      Conserved Domains (1) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
    18. NM_207040.1NP_996923.1  transcription factor 12 isoform c

      See identical proteins and their annotated locations for NP_996923.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has multiple differences in the 5' UTR and coding region compared to variant 1. This results in a shorter isoform (c) with a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AL831981, AU120213, BC050556, BC051769, BK001049, BX537967
      Consensus CDS
      CCDS42042.1
      UniProtKB/Swiss-Prot
      Q99081
      Related
      ENSP00000342459.3, ENST00000343827.7
      Conserved Domains (1) summary
      smart00353
      Location:413466
      HLH; helix loop helix domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p12 Primary Assembly

      Range
      56918090..57292595
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521960.3XP_011520262.1  transcription factor 12 isoform X1

      See identical proteins and their annotated locations for XP_011520262.1

      Conserved Domains (2) summary
      smart00353
      Location:619672
      HLH; helix loop helix domain
      pfam09786
      Location:287460
      CytochromB561_N; Cytochrome B561, N terminal
    2. XM_011521959.3XP_011520261.1  transcription factor 12 isoform X1

      See identical proteins and their annotated locations for XP_011520261.1

      Conserved Domains (2) summary
      smart00353
      Location:619672
      HLH; helix loop helix domain
      pfam09786
      Location:287460
      CytochromB561_N; Cytochrome B561, N terminal
    3. XM_011521961.3XP_011520263.1  transcription factor 12 isoform X2

      Conserved Domains (2) summary
      smart00353
      Location:618671
      HLH; helix loop helix domain
      pfam09786
      Location:287460
      CytochromB561_N; Cytochrome B561, N terminal
    4. XM_011521962.3XP_011520264.1  transcription factor 12 isoform X3

      Conserved Domains (1) summary
      smart00353
      Location:595648
      HLH; helix loop helix domain
    5. XM_011521963.3XP_011520265.1  transcription factor 12 isoform X4

      Conserved Domains (1) summary
      smart00353
      Location:594647
      HLH; helix loop helix domain
    6. XM_011521965.2XP_011520267.1  transcription factor 12 isoform X7

      Conserved Domains (2) summary
      smart00353
      Location:391444
      HLH; helix loop helix domain
      pfam09786
      Location:87232
      CytochromB561_N; Cytochrome B561, N terminal
    7. XM_017022520.2XP_016878009.1  transcription factor 12 isoform X5

    8. XM_011521967.2XP_011520269.1  transcription factor 12 isoform X9

      Conserved Domains (1) summary
      smart00353
      Location:367420
      HLH; helix loop helix domain
    9. XM_011521966.2XP_011520268.1  transcription factor 12 isoform X8

      Conserved Domains (2) summary
      smart00353
      Location:371424
      HLH; helix loop helix domain
      pfam09786
      Location:67212
      CytochromB561_N; Cytochrome B561, N terminal
    10. XM_011521969.1XP_011520271.1  transcription factor 12 isoform X6

      Conserved Domains (1) summary
      smart00353
      Location:412465
      HLH; helix loop helix domain
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