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

Gene ID: 7030, updated on 9-Feb-2020

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

Genomic context

See TFE3 in Genome Data Viewer
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_000023.11Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel subfamily D member 1 Neighboring gene GRIP1 associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 9113 Neighboring gene Sharpr-MPRA regulatory region 2669 Neighboring gene coiled-coil domain containing 120 Neighboring gene PRA1 domain family member 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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)

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

  1. NG_016297.2 RefSeqGene

    Range
    5104..19735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282142.2NP_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:239299
    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:327468
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:8160
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
  2. NM_006521.6NP_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:344404
    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:432573
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:113265
    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

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    49028726..49043357 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    cd00083
    Location:344378
    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:113265
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
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