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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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