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    Tcf12 transcription factor 12 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25720, updated on 18-Apr-2019

    Summary

    Official Symbol
    Tcf12provided by RGD
    Official Full Name
    transcription factor 12provided by RGD
    Primary source
    RGD:3829
    See related
    Ensembl:ENSRNOG00000057754
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    SCBPA; SCBP alpha
    Summary
    basic helix-loop-helix (bHLH) E-protein that recognizes the consensus binding site CANNTG (E-box); may be a transcriptional activator [RGD, Feb 2006]
    Annotation information
    Annotation category: suggests misassembly
    Expression
    Biased expression in Thymus (RPKM 380.3), Lung (RPKM 130.7) and 9 other tissues See more
    Orthologs

    Genomic context

    See Tcf12 in Genome Data Viewer
    Location:
    8q24
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (78343634..78657738, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 8 NC_005107.3 (74423476..74735375)

    Chromosome 8 - NC_005107.4Genomic Context describing neighboring genes Neighboring gene dynein light chain 1, cytoplasmic-like Neighboring gene cingulin-like 1 Neighboring gene uncharacterized LOC108351742 Neighboring gene uncharacterized LOC102546620

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Id Signaling Pathway, organism-specific biosystem (from WikiPathways)
      Id Signaling Pathway, organism-specific biosystemInhibitor of DNA binding (ID) proteins are members of the helix-loop-helix (HLH) family of proteins which lack a DNA binding domain themselves but bind to other family members inhibiting their DNA bi...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    E-box binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    E-box binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    HMG box domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    RNA polymerase II proximal promoter sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    RNA polymerase II proximal promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    SMAD binding IEA
    Inferred from Electronic Annotation
    more info
     
    SMAD binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    bHLH transcription factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    bHLH transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cAMP response element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein heterodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein heterodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    contributes_to transcription regulatory region DNA binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    RNA polymerase II transcription factor complex IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II transcription factor complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nuclear speck IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear speck ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleus TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transcription factor complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor 12
    Names
    DNA-binding protein HTF4
    E-box-binding protein
    SCBP-alpha
    TCF-12
    salivary-specific cAMP response element-binding protein alpha
    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.

    mRNA and Protein(s)

    1. NM_013176.2NP_037308.1  transcription factor 12

      See identical proteins and their annotated locations for NP_037308.1

      Status: PROVISIONAL

      Source sequence(s)
      L09656
      UniProtKB/Swiss-Prot
      P51514
      Related
      ENSRNOP00000074384.1, ENSRNOT00000081185.1
      Conserved Domains (1) summary
      smart00353
      Location:608661
      HLH; helix loop helix domain

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005107.4 Reference Rnor_6.0 Primary Assembly

      Range
      78343634..78657738 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017595483.1XP_017450972.1  transcription factor 12 isoform X3

    2. XM_006243345.2XP_006243407.1  transcription factor 12 isoform X1

      See identical proteins and their annotated locations for XP_006243407.1

      Conserved Domains (2) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
      pfam09786
      Location:275462
      CytochromB561_N; Cytochrome B561, N terminal
    3. XM_006243346.2XP_006243408.1  transcription factor 12 isoform X2

      UniProtKB/Swiss-Prot
      P51514
      Conserved Domains (1) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
    4. XM_006243350.2XP_006243412.1  transcription factor 12 isoform X7

      Conserved Domains (1) summary
      smart00353
      Location:582635
      HLH; helix loop helix domain
    5. XM_006243348.2XP_006243410.1  transcription factor 12 isoform X5

      Conserved Domains (1) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
    6. XM_006243349.2XP_006243411.1  transcription factor 12 isoform X6

      UniProtKB/Swiss-Prot
      P51514
      Conserved Domains (1) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
    7. XM_006243347.2XP_006243409.1  transcription factor 12 isoform X4

      Conserved Domains (1) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
    8. XM_017595485.1XP_017450974.1  transcription factor 12 isoform X10

    9. XM_017595484.1XP_017450973.1  transcription factor 12 isoform X9

    10. XM_006243351.1XP_006243413.1  transcription factor 12 isoform X8

      See identical proteins and their annotated locations for XP_006243413.1

      Conserved Domains (2) summary
      smart00353
      Location:550603
      HLH; helix loop helix domain
      pfam09786
      Location:217405
      CytochromB561_N; Cytochrome B561, N terminal
    11. XM_008766218.2XP_008764440.1  transcription factor 12 isoform X8

      See identical proteins and their annotated locations for XP_008764440.1

      Conserved Domains (2) summary
      smart00353
      Location:550603
      HLH; helix loop helix domain
      pfam09786
      Location:217405
      CytochromB561_N; Cytochrome B561, N terminal
    12. XM_017595486.1XP_017450975.1  transcription factor 12 isoform X9

    13. XM_006243354.3XP_006243416.1  transcription factor 12 isoform X14

      Conserved Domains (1) summary
      smart00353
      Location:447500
      HLH; helix loop helix domain
    14. XM_006243353.3XP_006243415.1  transcription factor 12 isoform X12

      Conserved Domains (2) summary
      smart00353
      Location:471524
      HLH; helix loop helix domain
      pfam09786
      Location:139326
      CytochromB561_N; Cytochrome B561, N terminal
    15. XM_008766219.2XP_008764441.1  transcription factor 12 isoform X13

      Conserved Domains (1) summary
      smart00353
      Location:448501
      HLH; helix loop helix domain
    16. XM_006243352.3XP_006243414.1  transcription factor 12 isoform X11

      Related
      ENSRNOP00000071744.1, ENSRNOT00000084925.1
      Conserved Domains (2) summary
      smart00353
      Location:472525
      HLH; helix loop helix domain
      pfam09786
      Location:139327
      CytochromB561_N; Cytochrome B561, N terminal

    Alternate Rn_Celera

    Genomic

    1. AC_000076.1 Alternate Rn_Celera

      Range
      68938004..69243587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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