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tfe3a transcription factor binding to IGHM enhancer 3a [ Danio rerio (zebrafish) ]

Gene ID: 114834, updated on 4-Jan-2025

Summary

Official Symbol
tfe3aprovided by ZNC
Official Full Name
transcription factor binding to IGHM enhancer 3aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-010919-2
See related
Ensembl:ENSDARG00000098903 AllianceGenome:ZFIN:ZDB-GENE-010919-2
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
cb873; zgc:109815
Summary
Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Acts upstream of or within DNA-templated transcription. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including hindbrain neural plate; intermediate cell mass of mesoderm; solid lens vesicle; ventral mesoderm; and yolk syncytial layer. 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, Jan 2025]
Orthologs
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Genomic context

See tfe3a in Genome Data Viewer
Location:
chromosome: 8
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (7778770..7809929)
105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (7739969..7770851)

Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC564674 Neighboring gene FYVE, RhoGEF and PH domain containing 1 Neighboring gene si:dkey-242k1.4 Neighboring gene uncharacterized LOC137496327 Neighboring gene zgc:113363

Genomic regions, transcripts, and products

Expression

  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

General gene information

Markers

Clone Names

  • MGC109815

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
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
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables protein dimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in nucleoplasm IC
Inferred by Curator
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

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)

  1. NM_131848.2NP_571923.2  transcription factor E3a

    Status: PROVISIONAL

    Source sequence(s)
    BC092697
    UniProtKB/TrEMBL
    Q561Z2
    Related
    ENSDARP00000135726.1, ENSDART00000171325.2
    Conserved Domains (3) summary
    cd00083
    Location:314374
    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:402538
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:101238
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007119.7 Reference GRCz11 Primary Assembly

    Range
    7778770..7809929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005166704.5XP_005166761.1  transcription factor E3a isoform X1

    UniProtKB/TrEMBL
    A0A8M2BE60
    Conserved Domains (3) summary
    cd00083
    Location:217277
    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:305441
    DUF3371; Domain of unknown function (DUF3371)
    pfam15951
    Location:4141
    MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus