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

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 transcription, DNA-templated. 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, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 8

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	8	NC_007119.7 (7778770..7810809)
105	previous assembly	GRCz10 (GCF_000002035.5)	8	NC_007119.6 (7739969..7770851)

Chromosome 8 - NC_007119.7 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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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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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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

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription	IDA Inferred from Direct Assay more info
acts_upstream_of_or_within regulation of DNA-templated transcription	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
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

General protein information

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Preferred Names: transcription factor E3; transcription factor E3a

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)

NM_131848.2 → NP_571923.2 transcription factor E3a

See identical proteins and their annotated locations for NP_571923.2

Status: PROVISIONAL

Source sequence(s)

BC092697

UniProtKB/TrEMBL

Q561Z2

Related

ENSDARP00000135726.1, ENSDART00000171325.2

Conserved Domains (3) summary

cd00083
Location:314 → 374

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:402 → 538

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:101 → 238

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

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007119.7 Reference GRCz11 Primary Assembly

Range

7778770..7810809

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005166704.4 → XP_005166761.1 transcription factor E3 isoform X1

UniProtKB/TrEMBL

A0A8M2BE60

Conserved Domains (3) summary

cd00083
Location:217 → 277

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:305 → 441

DUF3371; Domain of unknown function (DUF3371)

pfam15951
Location:4 → 141

MITF_TFEB_C_3_N; MITF/TFEB/TFEC/TFE3 N-terminus
XM_005166705.4 → XP_005166762.1 transcription factor E3 isoform X2

UniProtKB/TrEMBL

A0A8M2BE83

Related

ENSDARP00000139251.1, ENSDART00000161618.2

Conserved Domains (2) summary

cd00083
Location:67 → 127

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:155 → 291

DUF3371; Domain of unknown function (DUF3371)