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; AllianceGenome:HGNC:11752
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; MRXSPF; 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
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Genomic context

Location:: Xp11.23

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (49028726..49043357, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (48440314..48454961, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (48886237..48900883, complement)

Chromosome X - NC_000023.11 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: 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?

[Expression of SCD1 in TFE3-rRCC and its effect on proliferation and migration].
Title: [Expression of SCD1 in TFE3-rRCC and its effect on proliferation and migration].
Aberrant expression of TFE3 in granular cell tumor: Four cases in pediatrics.
Title: Aberrant expression of TFE3 in granular cell tumor: Four cases in pediatrics.
PEComa with ASPSCR1::TFE3 fusion: expanding the molecular genetic spectrum of TFE3-rearranged PEComa with an emphasis on overlap with alveolar soft part sarcoma.
Title: PEComa with ASPSCR1::TFE3 fusion: expanding the molecular genetic spectrum of TFE3-rearranged PEComa with an emphasis on overlap with alveolar soft part sarcoma.
Expression of TFE3 in Cellular and Myxoid Type of Neurothekeoma: Four Cases in Young Children and Adolescents.
Title: Expression of TFE3 in Cellular and Myxoid Type of Neurothekeoma: Four Cases in Young Children and Adolescents.
TFE3 Rearrangement and Expression in Renal Cell Carcinoma.
Title: TFE3 Rearrangement and Expression in Renal Cell Carcinoma.
PKM2 controls the translation of TFE3 to maintain the integrity of the Golgi apparatus for the survival of HeLa and ME-180 cervical cancer cells.
Title: PKM2 controls the translation of TFE3 to maintain the integrity of the Golgi apparatus for the survival of HeLa and ME-180 cervical cancer cells.
Cystic MED15::TFE3 translocation renal cell carcinoma: histologic mimicker of multilocular cystic renal neoplasm of low malignant potential with review of the literature.
Title: Cystic MED15::TFE3 translocation renal cell carcinoma: histologic mimicker of multilocular cystic renal neoplasm of low malignant potential with review of the literature.
RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome.
Title: RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome.
TFEB and TFE3 drive kidney cystogenesis and tumorigenesis.
Title: TFEB and TFE3 drive kidney cystogenesis and tumorigenesis.
A novel VCP::TFE3 gene fusion resulting from t(X;9)(p11.23;p13.3) chromosome translocation in TFE3 rearranged renal cancer cell carcinoma.
Title: A novel VCP::TFE3 gene fusion resulting from t(X;9)(p11.23;p13.3) chromosome translocation in TFE3 rearranged renal cancer cell carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (153)

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
Intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies MedGen: C5561930 OMIM: 301066 GeneReviews: Not available	not available
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

Go to the HIV-1, Human Interaction Database

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

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity 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	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein dimerization activity	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in humoral immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in lysosome organization	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity 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	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of brown fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of osteoclast differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in 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/TrEMBL

B4DIA5

Conserved Domains (3) summary

pfam11851
Location:327 → 468

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:8 → 161

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

cd18928
Location:232 → 322

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

A8MZL6, P19532, Q5JU74, Q92757, Q92758, Q99964

Related

ENSP00000314129.7, ENST00000315869.8

Conserved Domains (3) summary

pfam11851
Location:432 → 573

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:113 → 266

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

cd18928
Location:337 → 427

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

49028726..49043357 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024452432.2 → 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