Tfe3 transcription factor E3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tfe3provided by MGI
Official Full Name: transcription factor E3provided by MGI
Primary source: MGI:MGI:98511
See related: Ensembl:ENSMUSG00000000134 AllianceGenome:MGI:98511
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Tcfe3; Tfe-3; mTFE3; bHLHe33; F830016E06Rik
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. 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. Acts upstream of or within positive regulation of transcription, DNA-templated and regulation of osteoclast differentiation. Located in cytosol and nucleus. Is expressed in several structures, including adipose tissue; branchial arch; early conceptus; genitourinary system; and gut. 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, Apr 2022]
Expression: Ubiquitous expression in adrenal adult (RPKM 12.2), genital fat pad adult (RPKM 11.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: X A1.1; X 3.5 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (7628769..7641441)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (7762530..7775202)

Chromosome X - NC_000086.8 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The role of TFE3 in mediating skeletal muscle mitochondrial adaptations to exercise training.
Title: The role of TFE3 in mediating skeletal muscle mitochondrial adaptations to exercise training.
Dectin-1/CARD9 induction of the TFEB and TFE3 gene network is dispensable for phagocyte anti-Aspergillus activity in the lung.
Title: Dectin-1/CARD9 induction of the TFEB and TFE3 gene network is dispensable for phagocyte anti-Aspergillus activity in the lung.
TFEB and TFE3 control glucose homeostasis by regulating insulin gene expression.
Title: TFEB and TFE3 control glucose homeostasis by regulating insulin gene expression.
TFEB and TFE3 drive kidney cystogenesis and tumorigenesis.
Title: TFEB and TFE3 drive kidney cystogenesis and tumorigenesis.
Maintenance of neural stem-progenitor cells by the lysosomal biosynthesis regulators TFEB and TFE3 in the embryonic mouse telencephalon.
Title: Maintenance of neural stem-progenitor cells by the lysosomal biosynthesis regulators TFEB and TFE3 in the embryonic mouse telencephalon.
TFE3, a potential therapeutic target for Spinal Cord Injury via augmenting autophagy flux and alleviating ER stress.
Title: TFE3, a potential therapeutic target for Spinal Cord Injury via augmenting autophagy flux and alleviating ER stress.
Myeloid Folliculin balances mTOR activation to maintain innate immunity homeostasis.
Title: Myeloid Folliculin balances mTOR activation to maintain innate immunity homeostasis.
The Fnip1-deficient B cell progenitors exhibited increased nuclear localization of transcription factor binding to IgHM enhancer 3 (TFE3) in developing B cells, which correlated with an increased expression of TFE3-target genes, increased lysosome numbers and function, and increased autophagic flux.
Title: Folliculin Interacting Protein 1 Maintains Metabolic Homeostasis during B Cell Development by Modulating AMPK, mTORC1, and TFE3.
TFE3 Xp11.2 Translocation resulting in high TFE3 expression is associated with Renal Cell Carcinoma.
Title: TFE3 Xp11.2 Translocation Renal Cell Carcinoma Mouse Model Reveals Novel Therapeutic Targets and Identifies GPNMB as a Diagnostic Marker for Human Disease.
lysosome activity, the Ragulator protein complex, and the tumor-suppressor protein Folliculin enable the Rag GTPases C and D to bind and seclude the bHLH transcription factor Tfe3 in the cytoplasm.
Title: Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI851540 (e-PCR)
- UniSTS:181274

D1S3694 (e-PCR)
- UniSTS:474272

Tcfe3 (e-PCR), detects polymorphism
- UniSTS:144568

Tcfe3 (e-PCR), detects polymorphism
- UniSTS:496622

Tfe3 (e-PCR), detects polymorphism
- UniSTS:546045

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay 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	IDA Inferred from Direct Assay more info	PubMed
contributes_to protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in humoral immune response	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
involved_in lysosome organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cold-induced thermogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of brown fat cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell adhesion	ISO Inferred from Sequence Orthology 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 DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of osteoclast differentiation	IGI Inferred from Genetic Interaction more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in membrane	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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IC Inferred by Curator more info	PubMed

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_001105196.1 → NP_001098666.1 transcription factor E3 isoform b

See identical proteins and their annotated locations for NP_001098666.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AK139756, AL671995, BC056358

Consensus CDS

CCDS52985.1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

UniProtKB/TrEMBL

A2AEW0

Related

ENSMUSP00000078498.7, ENSMUST00000079542.13

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:466 → 535

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:112 → 260

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_001105197.1 → NP_001098667.1 transcription factor E3 isoform c

See identical proteins and their annotated locations for NP_001098667.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 3, 4, and 5 encode the same isoform (c).

Source sequence(s)

AK152221, BC056358, BY208269

Consensus CDS

CCDS72332.1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

Related

ENSMUSP00000111341.2, ENSMUST00000115677.8

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_001271489.1 → NP_001258418.1 transcription factor E3 isoform c

See identical proteins and their annotated locations for NP_001258418.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice site at an internal exon, compared to variant 1, and initiates translation at a downstream in-frame start codon. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 3, 4, and 5 encode the same isoform (c).

Source sequence(s)

AK159162, AL671995, BC056358

Consensus CDS

CCDS72332.1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

Related

ENSMUSP00000111343.2, ENSMUST00000115679.8

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_001271490.1 → NP_001258419.1 transcription factor E3 isoform c

See identical proteins and their annotated locations for NP_001258419.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an alternate splice site in the 5' exon, compared to variant 1, and initiates translation at a downstream in-frame start codon. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 3, 4, and 5 encode the same isoform (c).

Source sequence(s)

AK139756, AL671995, BC056358

Consensus CDS

CCDS72332.1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

Related

ENSMUSP00000134125.2, ENSMUST00000137467.8

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_001271491.1 → NP_001258420.1 transcription factor E3 isoform d

See identical proteins and their annotated locations for NP_001258420.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR, has multiple differences in the coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter than isoform a.

Source sequence(s)

AK155883, BC063047

Consensus CDS

CCDS72333.1

UniProtKB/TrEMBL

Q3U1L5

Related

ENSMUSP00000111342.3, ENSMUST00000115678.3

Conserved Domains (3) summary

cd18928
Location:196 → 286

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

pfam11851
Location:291 → 430

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 155

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_172472.3 → NP_766060.2 transcription factor E3 isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AF510653, AL671995, BC056358

Consensus CDS

CCDS52984.1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

UniProtKB/TrEMBL

A2AEW1

Related

ENSMUSP00000076864.4, ENSMUST00000077680.10

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:518 → 570

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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000086.8 Reference GRCm39 C57BL/6J

Range

7628769..7641441

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006527578.3 → XP_006527641.1 transcription factor E3 isoform X1

See identical proteins and their annotated locations for XP_006527641.1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_036161900.1 → XP_036017793.1 transcription factor E3 isoform X2

UniProtKB/TrEMBL

Q3U1L5

Conserved Domains (3) summary

cd18928
Location:196 → 286

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

pfam11851
Location:291 → 430

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 155

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_017318454.3 → XP_017173943.1 transcription factor E3 isoform X2

UniProtKB/TrEMBL

Q3U1L5

Conserved Domains (3) summary

cd18928
Location:196 → 286

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

pfam11851
Location:291 → 430

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 155

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_017318453.3 → XP_017173942.1 transcription factor E3 isoform X1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_036161898.1 → XP_036017791.1 transcription factor E3 isoform X1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_036161899.1 → XP_036017792.1 transcription factor E3 isoform X1

UniProtKB/Swiss-Prot

A2AEW3, A2AEW4, Q3U8H0, Q3UMV4, Q3UT52, Q64092, Q7TNC1, Q8BN29

Related

ENSMUSP00000099219.3, ENSMUST00000101695.9

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 → 465

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:7 → 160

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