ebf3a EBF transcription factor 3a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ebf3aprovided by ZNC
Official Full Name: EBF transcription factor 3aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-070112-292
See related: Ensembl:ENSDARG00000100244 AllianceGenome:ZFIN:ZDB-GENE-070112-292
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: ebf3; zgc:158829
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be located in nucleus. Is expressed in brain and sensory system. Human ortholog(s) of this gene implicated in hypotonia, ataxia, and delayed development syndrome. Orthologous to several human genes including EBF1 (EBF transcription factor 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 12

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (42436329..42578687)
105	previous assembly	GRCz10 (GCF_000002035.5)	12	NC_007123.6 (42281045..42423390)

Chromosome 12 - NC_007123.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

Data revealed that expression of DNA binding inhibitor 3, early B cell factor 2, Ebf3, Iroquois related homeobox 1, Kruppel-like factor 7 , mab-21-like 1 , fatty acid binding protein 7 and stathmin-like 4,were enriched in the diencephalon of zebrafish.
Title: Expression of ventral diencephalon-enriched genes in zebrafish.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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	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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in nervous system development	IEA Inferred from Electronic Annotation 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 nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: transcription factor COE3a

Names: early B cell factor 3a; early B-cell factor 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.

mRNA and Protein(s)

NM_001080602.1 → NP_001074071.1 transcription factor COE3a

See identical proteins and their annotated locations for NP_001074071.1

Status: PROVISIONAL

Source sequence(s)

BC129478

UniProtKB/TrEMBL

A0A0R4ISE7, A1L2E2, B2GPA4

Related

ENSDARP00000137939.1, ENSDART00000167324.2

Conserved Domains (3) summary

cd01175
Location:255 → 339

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:340 → 383

COE1_HLH; Transcription factor COE1 helix-loop-helix domain

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

NC_007123.7 Reference GRCz11 Primary Assembly

Range

42436329..42578687

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009306901.4 → XP_009305176.1 transcription factor COE3a isoform X1

UniProtKB/TrEMBL

A0A8M3BEC3

Conserved Domains (3) summary

cd01175
Location:264 → 348

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:349 → 392

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_009306905.4 → XP_009305180.1 transcription factor COE3a isoform X9

UniProtKB/TrEMBL

A0A8M3AYP6

Conserved Domains (3) summary

cd01175
Location:264 → 348

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:349 → 392

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_009306906.4 → XP_009305181.1 transcription factor COE3a isoform X13

UniProtKB/TrEMBL

A0A8M3BEC5

Conserved Domains (3) summary

cd01175
Location:264 → 348

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:349 → 392

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156408.5 → XP_005156465.1 transcription factor COE3a isoform X3

UniProtKB/TrEMBL

A0A8M2B3A0

Conserved Domains (3) summary

cd01175
Location:264 → 348

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:349 → 392

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156414.5 → XP_005156471.1 transcription factor COE3a isoform X10

UniProtKB/TrEMBL

A0A8M2B2S0

Conserved Domains (3) summary

cd01175
Location:264 → 348

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:349 → 392

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156416.5 → XP_005156473.1 transcription factor COE3a isoform X14

UniProtKB/TrEMBL

A0A8M2B369

Conserved Domains (3) summary

cd01175
Location:264 → 348

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:349 → 392

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_009306902.4 → XP_009305177.1 transcription factor COE3a isoform X2

UniProtKB/TrEMBL

A0A8M3AYM5

Conserved Domains (3) summary

cd01175
Location:263 → 347

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:348 → 391

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156409.5 → XP_005156466.1 transcription factor COE3a isoform X4

UniProtKB/TrEMBL

A0A8M2B362

Conserved Domains (3) summary

cd01175
Location:263 → 347

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:348 → 391

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_068224639.1 → XP_068080740.1 transcription factor COE3a isoform X11
XM_009306903.4 → XP_009305178.1 transcription factor COE3a isoform X5

UniProtKB/TrEMBL

A0A8M3B7N8

Conserved Domains (3) summary

cd01175
Location:255 → 339

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:340 → 383

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156411.5 → XP_005156468.1 transcription factor COE3a isoform X7

UniProtKB/TrEMBL

A0A286Y8W0, A0A8M2B2H2

Related

ENSDARP00000143395.2, ENSDART00000177303.2

Conserved Domains (3) summary

cd01175
Location:255 → 339

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:340 → 383

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_009306904.4 → XP_009305179.1 transcription factor COE3a isoform X6

UniProtKB/TrEMBL

A0A8M3B4V8

Conserved Domains (3) summary

cd01175
Location:254 → 338

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:339 → 382

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156412.5 → XP_005156469.1 transcription factor COE3a isoform X8

UniProtKB/TrEMBL

A0A8M2B2G9

Conserved Domains (3) summary

cd01175
Location:254 → 338

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:339 → 382

COE1_HLH; Transcription factor COE1 helix-loop-helix domain
XM_005156415.5 → XP_005156472.1 transcription factor COE3a isoform X12

UniProtKB/TrEMBL

A0A8M2B3A6

Conserved Domains (3) summary

cd01175
Location:254 → 338

IPT_COE; IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved ...

pfam16422
Location:21 → 247

COE1_DBD; Transcription factor COE1 DNA-binding domain

pfam16423
Location:339 → 382

COE1_HLH; Transcription factor COE1 helix-loop-helix domain