TFE3 transcription factor binding to IGHM enhancer 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TFE3provided by HGNC
Official Full Name: transcription factor binding to IGHM enhancer 3provided by HGNC
Primary source: HGNC:HGNC:11752
See related: Ensembl:ENSG00000068323 MIM:314310
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TFEA; RCCP2; RCCX1; bHLHe33
Summary: This gene encodes a basic helix-loop-helix domain-containing transcription factor that binds MUE3-type E-box sequences in the promoter of genes. The encoded protein promotes the expression of genes downstream of transforming growth factor beta (TGF-beta) signaling. This gene may be involved in chromosomal translocations in renal cell carcinomas and other cancers, resulting in the production of fusion proteins. Translocation partners include PRCC (papillary renal cell carcinoma), NONO (non-POU domain containing, octamer-binding), and ASPSCR1 (alveolar soft part sarcoma chromosome region, candidate 1), among other genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression: Ubiquitous expression in fat (RPKM 31.1), adrenal (RPKM 17.6) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: Xp11.23

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
109.20191205	current	GRCh38.p13 (GCF_000001405.39)	X	NC_000023.11 (49028726..49043357, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (48886237..48900990, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The present study suggests that the carcinogenesis of RBM10-TFE3 RCC in some, but not all, patients may be associated with chronic kidney disease.
Title: RBM10-TFE3 renal cell carcinoma characterised by paracentric inversion with consistent closely split signals in break-apart fluorescence in-situ hybridisation: study of 10 cases and a literature review.
This study reveal that TFE3 has a potential to serve as a diagnostic marker capable of assisting in the differential diagnosis of Desmoid-type fibromatosis (DTF) and other spindle cell lesions.
Title: Nuclear TFE3 expression is a diagnostic marker for Desmoid-type fibromatosis.
The results of our study and prior studies suggest that TFE3 immunohistochemistry should play only a minor role (if any) in the diagnosis of TFE3-rearranged tumors, with fluorescence in situ hybridization representing the preferred method.
Title: Immunohistochemistry for TFE3 lacks specificity and sensitivity in the diagnosis of TFE3-rearranged neoplasms: a comparative, 2-laboratory study.
Solid pseudopapillary neoplasms of the pancreas possibly originated from primordial pancreatic cells and overexpression of TFE3 was found in most cases.
Title: TFE3 is a diagnostic marker for solid pseudopapillary neoplasms of the pancreas.
Case Report: TFE3-rearranged PEComa without the customary morphology.
Title: Expanding the histomorphologic spectrum of TFE3-rearranged perivascular epithelioid cell tumors.
Our results indicated that the overexpressed TFE3 fusions were capable of escaping from the control by the mTOR signaling pathway and were accumulated in the nucleus in UOK109 and UOK120 cells. The nuclear retention of TFE3 fusions promoted the expression of lysosomal genes and other target genes, facilitating cancer cell resistance against an extreme environment.
Title: TFE3 fusions escape from controlling of mTOR signaling pathway and accumulate in the nucleus promoting genes expression in Xp11.2 translocation renal cell carcinomas.
Case Report: renal cell carcinoma with EWSR1-TFE3 fusion.
Title: A novel partner of TFE3 in the Xp11 translocation renal cell carcinoma: clinicopathological analyses and detection of EWSR1-TFE3 fusion.
Case Report: malignant perivascular epithelioid cell tumor of the oropharynx with strong TFE3 expression and gene rearrangement.
Title: Malignant perivascular epithelioid cell tumor of the oropharynx with strong TFE3 expression mimicking alveolar soft part sarcoma: a case report and review of the literature.
By morphologic, immunohistochemical, genetic, and prognostic similarities, alveolar soft-part sarcoma with the ASPSCR1-TFE3 gene fusion has a closer relationship with Xp11 neoplasm with melanocytic differentiation/TFE3 rearrangement-associated PEComa/melanotic Xp11 translocation renal cancer/melanotic Xp11 neoplasm
Title: Xp11 Translocation Renal Cell Carcinoma and the Mesenchymal Counterparts: An Evolving Concept with Novel Insights on Clinicopathologic Features, Prognosis, Treatment, and Classification.
Increased TFE3 expression in renal cell carcinoma was associated with poor progression-free survival regardless of the gene translocation status
Title: TFE3 translocation and protein expression in renal cell carcinoma are correlated with poor prognosis.

Submit: New GeneRIF Correction See all GeneRIFs (96)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Renal cell carcinoma, Xp11-associated MedGen: C3275446 OMIM: 300854 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of transcription factor binding to IGHM enhancer 3 (TFE3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-32925 (e-PCR)
- UniSTS:76174

DXS9891E (e-PCR)
- UniSTS:474546

PMC26398P1 (e-PCR)
- UniSTS:272336

DXS9784 (e-PCR)
- UniSTS:16851

DXS8225 (e-PCR)
- UniSTS:66797

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

Homology

Homologs of the TFE3 gene: The TFE3 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, and zebrafish.
Orthologs from Annotation Pipeline: 192 organisms have orthologs with human gene TFE3
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	NAS Non-traceable Author Statement more info	PubMed
RNA polymerase II proximal promoter sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein dimerization activity	IEA Inferred from Electronic Annotation more info
transcription regulatory region DNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
adaptive immune response	IEA Inferred from Electronic Annotation more info
humoral immune response	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
positive regulation of cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of transcription, DNA-templated	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of osteoclast differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytosol	IDA Inferred from Direct Assay more info
nuclear chromatin	ISA Inferred from Sequence Alignment more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: transcription factor E3

Names: class E basic helix-loop-helix protein 33; transcription factor E family, member A; transcription factor for IgH enhancer; transcription factor for immunoglobulin heavy-chain enhancer 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.

Genomic

NG_016297.2 RefSeqGene

Range

5104..19735

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001282142.2 → NP_001269071.1 transcription factor E3 isoform 2

See identical proteins and their annotated locations for NP_001269071.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AL161985, BM904206, HY157114

UniProtKB/Swiss-Prot

P19532

UniProtKB/TrEMBL

B4DIA5

Conserved Domains (3) summary

cd00083
Location:239 → 299

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:327 → 468

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:8 → 160

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
NM_006521.6 → NP_006512.2 transcription factor E3 isoform 1

See identical proteins and their annotated locations for NP_006512.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL161985, BC026027, BM904206, HY157114

Consensus CDS

CCDS14315.3

UniProtKB/Swiss-Prot

P19532

UniProtKB/TrEMBL

A0A024QZ23

Related

ENSP00000314129.7, ENST00000315869.8

Conserved Domains (3) summary

cd00083
Location:344 → 404

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:432 → 573

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:113 → 265

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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p13 Primary Assembly

Range

49028726..49043357 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024452432.1 → XP_024308200.1 transcription factor E3 isoform X1

Conserved Domains (2) summary

cd00083
Location:344 → 378

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, ...

pfam15951
Location:113 → 265

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