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

    Gene ID: 7030, updated on 5-Feb-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TFE3 in Genome Data Viewer
    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_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 12141 Neighboring gene potassium voltage-gated channel subfamily D member 1 Neighboring gene GRIP1 associated protein 1 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:48840212-48840468 Neighboring gene Sharpr-MPRA regulatory region 9113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29627 Neighboring gene CRISPRi-FlowFISH-validated HDAC6 regulatory element 4 Neighboring gene Sharpr-MPRA regulatory region 2669 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:48900209-48901072 Neighboring gene CRISPRi-FlowFISH-validated PQBP1 regulatory element 4 Neighboring gene Sharpr-MPRA regulatory region 13918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20833 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

    Gene Ontology Provided by GOA

    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

    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)

    NEW Try the new Transcript table

    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/TrEMBL
      B4DIA5
      Conserved Domains (3) summary
      pfam11851
      Location:327468
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:8161
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18928
      Location:232322
      bHLHzip_TFE3; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins
    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
      A8MZL6, P19532, Q5JU74, Q92757, Q92758, Q99964
      Related
      ENSP00000314129.7, ENST00000315869.8
      Conserved Domains (3) summary
      pfam11851
      Location:432573
      DUF3371; Domain of unknown function (DUF3371)
      pfam15951
      Location:113266
      MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
      cd18928
      Location:337427
      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

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_024452432.2XP_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

    RNA

    1. XR_007068199.1 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791820.1 Reference GRCh38.p14 PATCHES

      Range
      187561..202192 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333412.1XP_054189387.1  transcription factor E3 isoform X1

    RNA

    1. XR_008485836.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      48440314..48454961 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327658.1XP_054183633.1  transcription factor E3 isoform X1

    RNA

    1. XR_008485505.1 RNA Sequence