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

Gene ID: 25720, updated on 27-Nov-2024

Summary

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Official Symbol
Tcf12provided by RGD
Official Full Name
transcription factor 12provided by RGD
Primary source
RGD:3829
See related
EnsemblRapid:ENSRNOG00000057754 AllianceGenome:RGD:3829
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
Enables HMG box domain binding activity and cAMP response element binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in nucleus. Human ortholog(s) of this gene implicated in craniosynostosis and hypogonadotropic hypogonadism. Orthologous to human TCF12 (transcription factor 12). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 380.3), Lung (RPKM 130.7) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Tcf12 in Genome Data Viewer
Location:
8q24
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (81371201..81682337, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (72490447..72799265, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (78343634..78657738, complement)

Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene dynein light chain LC8-type 1, pseudogene 1 Neighboring gene cingulin-like 1 Neighboring gene uncharacterized LOC134480205 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC134479978

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. The E protein HEB is preferentially expressed in developing muscle. Conway K, et al. Differentiation, 2004 Sep. PMID 15554944
  2. Tissue-specific RNA splicing generates an ankyrin-like domain that affects the dimerization and DNA-binding properties of a bHLH protein. Klein ES, et al. Genes Dev, 1993 Jan. PMID 8422988
  3. The helix-loop-helix proteins (salivary-specific cAMP response element-binding proteins) can modulate cAMP-inducible RP4 gene expression in salivary cells. Lin HH, et al. J Biol Chem, 1993 May 15. PMID 7683670
  4. Enhanced expression of Pctk1, Tcf12 and Ccnd1 in hippocampus of rats: Impact on cognitive function, synaptic plasticity and pathology. Wu K, et al. Neurobiol Learn Mem, 2012 Jan. PMID 21982980, Free PMC Article
  5. Murine helix-loop-helix transcriptional activator proteins binding to the E-box motif of the Akv murine leukemia virus enhancer identified by cDNA cloning. Nielsen AL, et al. Mol Cell Biol, 1992 Aug. PMID 1321336, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The learning and memory deficits in Tcf12 animals are likely due to neuropathology associated with Tcf12 gene expression.
    Title: Enhanced expression of Pctk1, Tcf12 and Ccnd1 in hippocampus of rats: Impact on cognitive function, synaptic plasticity and pathology.
  2. HEB is implicated in the development of skeletal muscle (HEB).
    Title: The E protein HEB is preferentially expressed in developing muscle.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
  
enables E-box binding ISO
Inferred from Sequence Orthology
more info
  
enables E-box binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables HMG box domain binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables SMAD binding ISO
Inferred from Sequence Orthology
more info
  
enables bHLH transcription factor binding ISO
Inferred from Sequence Orthology
more info
  
enables cAMP response element binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables protein heterodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
contributes_to transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of gene expression ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of neuron differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to gonadotropin-releasing hormone ISO
Inferred from Sequence Orthology
more info
  
involved_in response to gonadotropin-releasing hormone ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex ISO
Inferred from Sequence Orthology
more info
  
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromatin ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
  

General protein information

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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)

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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_013176.2 → NP_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, ENSRNOT00000081185.3
    Conserved Domains (1) summary
    smart00353
    Location:608 → 661
    HLH; helix loop helix domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086026.1 Reference GRCr8

    Range
    81371201..81682337 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006243350.4 → XP_006243412.1  transcription factor 12 isoform X11

    Conserved Domains (1) summary
    smart00353
    Location:582 → 635
    HLH; helix loop helix domain

  2. XM_039080907.2 → XP_038936835.1  transcription factor 12 isoform X12

    Conserved Domains (1) summary
    cd18945
    Location:570 → 654
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  3. XM_006243348.4 → XP_006243410.1  transcription factor 12 isoform X8

    Conserved Domains (1) summary
    smart00353
    Location:583 → 636
    HLH; helix loop helix domain

  4. XM_017595483.3 → XP_017450972.1  transcription factor 12 isoform X4

  5. XM_039080905.2 → XP_038936833.1  transcription factor 12 isoform X5

    Conserved Domains (1) summary
    cd18945
    Location:594 → 678
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  6. XM_006243345.4 → XP_006243407.1  transcription factor 12 isoform X1

    See identical proteins and their annotated locations for XP_006243407.1

    UniProtKB/TrEMBL
    A6KEQ2
    Conserved Domains (2) summary
    smart00353
    Location:607 → 660
    HLH; helix loop helix domain
    pfam09786
    Location:275 → 462
    CytochromB561_N; Cytochrome B561, N terminal

  7. XM_006243349.4 → XP_006243411.1  transcription factor 12 isoform X10

    UniProtKB/Swiss-Prot
    P51514
    Conserved Domains (1) summary
    smart00353
    Location:583 → 636
    HLH; helix loop helix domain

  8. XM_039080906.2 → XP_038936834.1  transcription factor 12 isoform X9

    Conserved Domains (1) summary
    cd18945
    Location:571 → 655
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  9. XM_006243347.4 → XP_006243409.1  transcription factor 12 isoform X7

    UniProtKB/TrEMBL
    A0A0G2KB53
    Related
    ENSRNOP00000075657.2, ENSRNOT00000087270.3
    Conserved Domains (1) summary
    smart00353
    Location:584 → 637
    HLH; helix loop helix domain

  10. XM_063264980.1 → XP_063121050.1  transcription factor 12 isoform X6

  11. XM_006243346.4 → XP_006243408.1  transcription factor 12 isoform X2

    UniProtKB/Swiss-Prot
    P51514
    Conserved Domains (1) summary
    smart00353
    Location:607 → 660
    HLH; helix loop helix domain

  12. XM_039080904.2 → XP_038936832.1  transcription factor 12 isoform X3

    Conserved Domains (1) summary
    cd18945
    Location:595 → 679
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  13. XM_006243351.3 → XP_006243413.1  transcription factor 12 isoform X13

    See identical proteins and their annotated locations for XP_006243413.1

    Related
    ENSRNOP00000106756.1, ENSRNOT00000136287.1
    Conserved Domains (2) summary
    smart00353
    Location:550 → 603
    HLH; helix loop helix domain
    pfam09786
    Location:217 → 405
    CytochromB561_N; Cytochrome B561, N terminal

  14. XM_017595485.3 → XP_017450974.1  transcription factor 12 isoform X15

  15. XM_017595484.3 → XP_017450973.1  transcription factor 12 isoform X14

  16. XM_006243354.4 → XP_006243416.1  transcription factor 12 isoform X19

    UniProtKB/TrEMBL
    A0A0G2K188
    Conserved Domains (1) summary
    smart00353
    Location:447 → 500
    HLH; helix loop helix domain

  17. XM_006243353.4 → XP_006243415.1  transcription factor 12 isoform X17

    UniProtKB/TrEMBL
    A0A0G2K188
    Conserved Domains (2) summary
    smart00353
    Location:471 → 524
    HLH; helix loop helix domain
    pfam09786
    Location:139 → 326
    CytochromB561_N; Cytochrome B561, N terminal

  18. XM_063264982.1 → XP_063121052.1  transcription factor 12 isoform X22

  19. XM_039080908.2 → XP_038936836.1  transcription factor 12 isoform X20

    UniProtKB/TrEMBL
    A0A0G2K188
    Conserved Domains (1) summary
    cd18945
    Location:435 → 519
    bHLH_E-protein_TCF4_E2-2; basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins

  20. XM_008766219.3 → XP_008764441.1  transcription factor 12 isoform X18

    UniProtKB/TrEMBL
    A0A0G2K188
    Conserved Domains (1) summary
    smart00353
    Location:448 → 501
    HLH; helix loop helix domain

  21. XM_063264981.1 → XP_063121051.1  transcription factor 12 isoform X21

  22. XM_006243352.4 → XP_006243414.1  transcription factor 12 isoform X16

    UniProtKB/TrEMBL
    A0A0G2K188
    Related
    ENSRNOP00000071744.1, ENSRNOT00000084925.3
    Conserved Domains (2) summary
    smart00353
    Location:472 → 525
    HLH; helix loop helix domain
    pfam09786
    Location:139 → 327
    CytochromB561_N; Cytochrome B561, N terminal
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51514.1 GenPept UniProtKB/Swiss-Prot:P51514

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