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

Summary

Official Symbol: Tcf12provided by RGD
Official Full Name: transcription factor 12provided by RGD
Primary source: RGD:3829
See related: Ensembl: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. Orthologous to human TCF12 (transcription factor 12). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 380.3), Lung (RPKM 130.7) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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

General gene information

Go to the top of the page Help

Markers

Tcf12 (e-PCR), detects polymorphism
- UniSTS:546568

Tcf12 (e-PCR), detects polymorphism
- UniSTS:547157

Tcf12 (e-PCR), detects polymorphism
- UniSTS:144555

RH94512 (e-PCR)
- UniSTS:119760

Tcf12 (e-PCR), detects polymorphism
- UniSTS:256494

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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
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
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of 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	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

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

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, ENSRNOT00000081185.2

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

NC_086026.1 Reference GRCr8

Range

81371201..81682337 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

smart00353
Location:582 → 635

HLH; helix loop helix domain
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
XM_006243348.4 → XP_006243410.1 transcription factor 12 isoform X8

Conserved Domains (1) summary

smart00353
Location:583 → 636

HLH; helix loop helix domain
XM_017595483.3 → XP_017450972.1 transcription factor 12 isoform X4
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
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
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
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
XM_006243347.4 → XP_006243409.1 transcription factor 12 isoform X7

UniProtKB/TrEMBL

A0A0G2KB53

Related

ENSRNOP00000075657.2

Conserved Domains (1) summary

smart00353
Location:584 → 637

HLH; helix loop helix domain
XM_063264980.1 → XP_063121050.1 transcription factor 12 isoform X6
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
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
XM_006243351.3 → XP_006243413.1 transcription factor 12 isoform X13

See identical proteins and their annotated locations for XP_006243413.1

Conserved Domains (2) summary

smart00353
Location:550 → 603

HLH; helix loop helix domain

pfam09786
Location:217 → 405

CytochromB561_N; Cytochrome B561, N terminal
XM_017595485.3 → XP_017450974.1 transcription factor 12 isoform X15
XM_017595484.3 → XP_017450973.1 transcription factor 12 isoform X14
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
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
XM_063264982.1 → XP_063121052.1 transcription factor 12 isoform X22

UniProtKB/TrEMBL

A0A0G2K188
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
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
XM_063264981.1 → XP_063121051.1 transcription factor 12 isoform X21

UniProtKB/TrEMBL

A0A0G2K188
XM_006243352.4 → XP_006243414.1 transcription factor 12 isoform X16

UniProtKB/TrEMBL

A0A0G2K188

Related

ENSRNOP00000071744.1

Conserved Domains (2) summary

smart00353
Location:472 → 525

HLH; helix loop helix domain

pfam09786
Location:139 → 327

CytochromB561_N; Cytochrome B561, N terminal