Tfe3 transcription factor binding to IGHM enhancer 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tfe3provided by RGD
Official Full Name: transcription factor binding to IGHM enhancer 3provided by RGD
Primary source: RGD:1559642
See related: EnsemblRapid:ENSRNOG00000009605 AllianceGenome:RGD:1559642
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: Tcfe3; RGD1559642
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; E-box binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including negative regulation of cold-induced thermogenesis; positive regulation of brown fat cell differentiation; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of DNA-templated transcription and regulation of osteoclast differentiation. Predicted to be located in cytosol; lysosomal membrane; and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in renal cell carcinoma. Orthologous to human TFE3 (transcription factor binding to IGHM enhancer 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Adrenal (RPKM 52.1), Lung (RPKM 45.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: Xq12

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (17401466..17414829, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (14729547..14742830, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (15574579..15587826, complement)

Chromosome X - NC_086039.1 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?

MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B.
Title: MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B.
TFE3 activation by mTORC1 signaling is involved in the development of abnormal ductal structures in Tsc2 knockout teratomas.
Title: Aberrant differentiation of Tsc2-deficient teratomas associated with activation of the mTORC1-TFE3 pathway.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	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 activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables E-box binding	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 protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in humoral immune response	ISO Inferred from Sequence Orthology more info
involved_in lysosome organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of brown fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of osteoclast differentiation	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

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: transcription factor E3

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_001271227.1 → NP_001258156.1 transcription factor E3

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000021

UniProtKB/TrEMBL

D3ZAW6

Related

ENSRNOP00000012830.6, ENSRNOT00000012829.8

Conserved Domains (3) summary

cd00083
Location:343 → 403

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam11851
Location:431 → 571

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:112 → 264

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

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_086039.1 Reference GRCr8

Range

17401466..17414829 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006256728.5 → XP_006256790.1 transcription factor E3 isoform X3

See identical proteins and their annotated locations for XP_006256790.1

UniProtKB/TrEMBL

A0A8I5ZU56, D3ZAW6

Conserved Domains (3) summary

cd18928
Location:231 → 321

bHLHzip_TFE3; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins

pfam11851
Location:326 → 466

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_006256722.4 → XP_006256784.1 transcription factor E3 isoform X2

UniProtKB/TrEMBL

A0A8I5ZU56

Related

ENSRNOP00000080987.2, ENSRNOT00000104339.2

Conserved Domains (3) summary

cd00083
Location:308 → 368

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam11851
Location:396 → 536

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:112 → 260

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_006256727.5 → XP_006256789.1 transcription factor E3 isoform X3

See identical proteins and their annotated locations for XP_006256789.1

UniProtKB/TrEMBL

A0A8I5ZU56, D3ZAW6

Conserved Domains (3) summary

cd18928
Location:231 → 321

bHLHzip_TFE3; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins

pfam11851
Location:326 → 466

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_006256721.5 → XP_006256783.1 transcription factor E3 isoform X1

UniProtKB/TrEMBL

A0A8I5ZPP5, A0A8I5ZU56

Related

ENSRNOP00000080433.1, ENSRNOT00000100614.2

Conserved Domains (3) summary

cd00083
Location:309 → 369

HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

pfam11851
Location:397 → 537

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:78 → 230

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_039099777.2 → XP_038955705.1 transcription factor E3 isoform X3

UniProtKB/TrEMBL

A0A8I5ZU56, D3ZAW6

Conserved Domains (3) summary

cd18928
Location:231 → 321

bHLHzip_TFE3; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins

pfam11851
Location:326 → 466

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_063280052.1 → XP_063136122.1 transcription factor E3 isoform X5
XM_063280053.1 → XP_063136123.1 transcription factor E3 isoform X7
XM_039099778.2 → XP_038955706.1 transcription factor E3 isoform X4

Conserved Domains (1) summary

pfam15951
Location:112 → 265

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_039099779.2 → XP_038955707.1 transcription factor E3 isoform X6

Conserved Domains (1) summary

pfam15951
Location:112 → 260

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus