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Tbx3 T-box transcription factor 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 353305, updated on 27-Nov-2024

Summary

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Official Symbol: Tbx3provided by RGD
Official Full Name: T-box transcription factor 3provided by RGD
Primary source: RGD:735203
See related: EnsemblRapid:ENSRNOG00000008706 AllianceGenome:RGD:735203
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in negative regulation of apoptotic process. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be part of transcription regulator complex. Predicted to be active in cilium and nucleus. Biomarker of myocardial infarction. Human ortholog(s) of this gene implicated in ulnar-mammary syndrome. Orthologous to human TBX3 (T-box transcription factor 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 379.4), Lung (RPKM 114.2) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

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See Tbx3 in Genome Data Viewer

Location:: 12q16

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	12	NC_086030.1 (42540378..42555490, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	12	NC_051347.1 (36879924..36894849, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	12	NC_005111.4 (42479518..42494588, complement)

Chromosome 12 - NC_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation 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 repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior axis specification, embryo	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior axis specification, embryo	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within atrioventricular bundle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in atrioventricular canal development	ISO Inferred from Sequence Orthology more info
involved_in atrioventricular canal morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blood vessel development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within branching involved in mammary gland duct morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cardiac epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in cardiac jelly development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac muscle cell fate commitment	ISO Inferred from Sequence Orthology more info
involved_in cell fate specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cellular senescence	ISO Inferred from Sequence Orthology more info
involved_in cellular senescence	ISO Inferred from Sequence Orthology more info
involved_in cellular senescence	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic digit morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic forelimb morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within embryonic heart tube development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic hindlimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in endocardial cushion formation	ISO Inferred from Sequence Orthology more info
involved_in female genitalia development	ISO Inferred from Sequence Orthology more info
involved_in female genitalia development	ISS Inferred from Sequence or Structural Similarity more info
involved_in follicle-stimulating hormone secretion	ISO Inferred from Sequence Orthology more info
involved_in follicle-stimulating hormone secretion	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart looping	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of hepatoblast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limbic system development	ISO Inferred from Sequence Orthology more info
involved_in luteinizing hormone secretion	ISO Inferred from Sequence Orthology more info
involved_in luteinizing hormone secretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in male genitalia development	ISO Inferred from Sequence Orthology more info
involved_in male genitalia development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within mammary gland development	ISO Inferred from Sequence Orthology more info
involved_in mammary gland development	ISO Inferred from Sequence Orthology more info
involved_in mammary gland development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within mammary placode formation	ISO Inferred from Sequence Orthology more info
involved_in mesoderm morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in mesoderm morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell proliferation involved in heart morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myoblast differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within outflow tract morphogenesis	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
involved_in positive regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein complex stability	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein stability	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
acts_upstream_of_or_within roof of mouth development	ISO Inferred from Sequence Orthology more info
involved_in semicircular canal morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sinoatrial node cell development	ISO Inferred from Sequence Orthology more info
involved_in sinoatrial node cell development	ISO Inferred from Sequence Orthology more info
involved_in skeletal system development	ISO Inferred from Sequence Orthology more info
involved_in skeletal system development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within smooth muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within specification of animal organ position	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of stem cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ureteric peristalsis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular septum morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cilium	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: T-box transcription factor TBX3

Names: T-box 3 (ulnar mammary syndrome); T-box protein 3

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)

NM_181638.3 → NP_853669.1 T-box transcription factor TBX3

See identical proteins and their annotated locations for NP_853669.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000012

UniProtKB/Swiss-Prot

Q7TST9

UniProtKB/TrEMBL

A6J1K4

Related

ENSRNOP00000011552.2, ENSRNOT00000011552.6

Conserved Domains (2) summary

pfam12598
Location:323 → 404

TBX; T-box transcription factor

cd20188
Location:101 → 305

T-box_TBX2_3-like; DNA-binding domain of T-box transcription factor 2 and 3, and related T-box proteins

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_086030.1 Reference GRCr8

Range

42540378..42555490 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063271423.1 → XP_063127493.1 T-box transcription factor TBX3 isoform X2

UniProtKB/TrEMBL

A0A0G2K8D7
XM_006249416.5 → XP_006249478.1 T-box transcription factor TBX3 isoform X1

See identical proteins and their annotated locations for XP_006249478.1

UniProtKB/Swiss-Prot

Q7TST9

UniProtKB/TrEMBL

A6J1K4

Conserved Domains (2) summary

pfam12598
Location:323 → 404

TBX; T-box transcription factor

cd20188
Location:101 → 305

T-box_TBX2_3-like; DNA-binding domain of T-box transcription factor 2 and 3, and related T-box proteins
XM_006249418.3 → XP_006249480.1 T-box transcription factor TBX3 isoform X2

UniProtKB/TrEMBL

A0A0G2K8D7

Related

ENSRNOP00000074567.1, ENSRNOT00000084018.3

Conserved Domains (2) summary

pfam12598
Location:303 → 393

TBX; T-box transcription factor

cd00182
Location:102 → 287

TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
XM_063271422.1 → XP_063127492.1 T-box transcription factor TBX3 isoform X1

UniProtKB/Swiss-Prot

Q7TST9

UniProtKB/TrEMBL

A6J1K4
XM_006249417.5 → XP_006249479.1 T-box transcription factor TBX3 isoform X1

See identical proteins and their annotated locations for XP_006249479.1

UniProtKB/Swiss-Prot

Q7TST9

UniProtKB/TrEMBL

A6J1K4

Conserved Domains (2) summary

pfam12598
Location:323 → 404

TBX; T-box transcription factor

cd20188
Location:101 → 305

T-box_TBX2_3-like; DNA-binding domain of T-box transcription factor 2 and 3, and related T-box proteins