rerea arginine-glutamic acid dipeptide (RE) repeats a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rereaprovided by ZNC
Official Full Name: arginine-glutamic acid dipeptide (RE) repeats aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-060718-1
See related: Ensembl:ENSDARG00000077353 AllianceGenome:ZFIN:ZDB-GENE-060718-1
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: rere; atrophin2
Summary: Enables transcription corepressor binding activity. Acts upstream of or within several processes, including closure of optic fissure; pharyngeal system development; and regulation of signal transduction. Predicted to be active in nucleus. Is expressed in several structures, including germ ring; gut; head; nervous system; and pectoral fin bud. Orthologous to human RERE (arginine-glutamic acid dipeptide repeats). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 23

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (22690374..22928600)
105	previous assembly	GRCz10 (GCF_000002035.5)	23	NC_007134.6 (22763773..23002049)

Chromosome 23 - NC_007134.7 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?

Zebrafish model of RERE syndrome recapitulates key ophthalmic defects that are rescued by small molecule inhibitor of shh signaling.
Title: Zebrafish model of RERE syndrome recapitulates key ophthalmic defects that are rescued by small molecule inhibitor of shh signaling.
Results suggest that atrophin2 plays a role in the feedback regulation of Fgf8 signaling.
Title: Mutation of the atrophin2 gene in the zebrafish disrupts signaling by fibroblast growth factor during development of the inner ear.
the Atro-Rpd3 complex plays a conserved role to function as a Ci(R) corepressor.
Title: Atrophin-Rpd3 complex represses Hedgehog signaling by acting as a corepressor of CiR.
Tissue-specific transcriptional repression, by means of an REREa-Histone Deacetylase complex, modulates growth factor signaling during embryogenesis.
Title: REREa/Atrophin-2 interacts with histone deacetylase and Fgf8 signaling to regulate multiple processes of zebrafish development.

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General gene information

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Markers

G38908 (e-PCR)
- UniSTS:29773

G47125 (e-PCR)
- UniSTS:107914

G38907 (e-PCR)
- UniSTS:14073

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables transcription corepressor activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription corepressor binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within closure of optic fissure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of smoothened signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pharyngeal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pharyngeal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of fibroblast growth factor receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of fibroblast growth factor receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
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: arginine-glutamic acid dipeptide repeats protein

Names: atrophin 2; bab; babyface; gap; gaping mouth; rereb

NCBI Reference Sequences (RefSeq)

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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_007134.7 Reference GRCz11 Primary Assembly

Range

22690374..22928600

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021469958.2 → XP_021325633.1 arginine-glutamic acid dipeptide repeats protein isoform X1

UniProtKB/TrEMBL

A0A8M2B939, E7F226

Conserved Domains (5) summary

cd11661
Location:352 → 397

SANT_MTA3_like; Myb-Like Dna-Binding Domain of MTA3 and related proteins

smart00401
Location:460 → 509

ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]

cd04709
Location:101 → 264

BAH_MTA; BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH ...

pfam01448
Location:243 → 293

ELM2; ELM2 domain

cl26464
Location:525 → 1530

Atrophin-1; Atrophin-1 family
XM_005162203.5 → XP_005162260.1 arginine-glutamic acid dipeptide repeats protein isoform X1

See identical proteins and their annotated locations for XP_005162260.1

UniProtKB/TrEMBL

A0A8M2B939, E7F226

Related

ENSDARP00000102789.2, ENSDART00000111345.4

Conserved Domains (5) summary

cd11661
Location:352 → 397

SANT_MTA3_like; Myb-Like Dna-Binding Domain of MTA3 and related proteins

smart00401
Location:460 → 509

ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]

cd04709
Location:101 → 264

BAH_MTA; BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH ...

pfam01448
Location:243 → 293

ELM2; ELM2 domain

cl26464
Location:525 → 1530

Atrophin-1; Atrophin-1 family
XM_009296906.4 → XP_009295181.1 arginine-glutamic acid dipeptide repeats protein isoform X2

UniProtKB/TrEMBL

A0A8M3AYH4

Conserved Domains (7) summary

smart00717
Location:353 → 398

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

cd11661
Location:352 → 397

SANT_MTA3_like; Myb-Like Dna-Binding Domain of MTA3 and related proteins

smart00401
Location:460 → 509

ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]

cd00202
Location:463 → 517

ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C

cd04709
Location:101 → 264

BAH_MTA; BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH ...

pfam01448
Location:243 → 293

ELM2; ELM2 domain

pfam03154
Location:525 → 1520

Atrophin-1; Atrophin-1 family
XM_005162201.5 → XP_005162258.1 arginine-glutamic acid dipeptide repeats protein isoform X1

See identical proteins and their annotated locations for XP_005162258.1

UniProtKB/TrEMBL

A0A8M2B939, E7F226

Conserved Domains (5) summary

cd11661
Location:352 → 397

SANT_MTA3_like; Myb-Like Dna-Binding Domain of MTA3 and related proteins

smart00401
Location:460 → 509

ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]

cd04709
Location:101 → 264

BAH_MTA; BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH ...

pfam01448
Location:243 → 293

ELM2; ELM2 domain

cl26464
Location:525 → 1530

Atrophin-1; Atrophin-1 family
XM_068216904.1 → XP_068073005.1 arginine-glutamic acid dipeptide repeats protein isoform X4
XM_005162204.5 → XP_005162261.1 arginine-glutamic acid dipeptide repeats protein isoform X3

UniProtKB/TrEMBL

A0A8M2B917

Related

ENSDARP00000117039.1, ENSDART00000135130.2

Conserved Domains (7) summary

smart00717
Location:353 → 398

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

cd11661
Location:352 → 397

SANT_MTA3_like; Myb-Like Dna-Binding Domain of MTA3 and related proteins

smart00401
Location:460 → 509

ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]

cd00202
Location:463 → 517

ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C

cd04709
Location:101 → 264

BAH_MTA; BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH ...

pfam01448
Location:243 → 293

ELM2; ELM2 domain

pfam03154
Location:525 → 1520

Atrophin-1; Atrophin-1 family
XM_001922746.7 → XP_001922781.3 arginine-glutamic acid dipeptide repeats protein isoform X5

UniProtKB/TrEMBL

A0A8M1QLN1

Conserved Domains (7) summary

smart00717
Location:128 → 173

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

cd11661
Location:127 → 172

SANT_MTA3_like; Myb-Like Dna-Binding Domain of MTA3 and related proteins

smart00401
Location:235 → 284

ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]

cd00202
Location:238 → 292

ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C

pfam01448
Location:18 → 68

ELM2; ELM2 domain

pfam03154
Location:300 → 1305

Atrophin-1; Atrophin-1 family

cl02608
Location:8 → 39

BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...

Reference GRCz11 ALT_DRER_TU_1

Genomic

NW_018395147.1 Reference GRCz11 ALT_DRER_TU_1

Range

3550..153675

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021473677.2 → XP_021329352.1 arginine-glutamic acid dipeptide repeats protein isoform X6

UniProtKB/TrEMBL

A0A8M9PWY0

Conserved Domains (1) summary

cl02608
Location:101 → 133

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
XM_021473678.2 → XP_021329353.1 arginine-glutamic acid dipeptide repeats protein isoform X6

UniProtKB/TrEMBL

A0A8M9PWY0

Conserved Domains (1) summary

cl02608
Location:101 → 133

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
XM_021473679.2 → XP_021329354.1 arginine-glutamic acid dipeptide repeats protein isoform X6

UniProtKB/TrEMBL

A0A8M9PWY0

Conserved Domains (1) summary

cl02608
Location:101 → 133

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
XM_021473676.2 → XP_021329351.1 arginine-glutamic acid dipeptide repeats protein isoform X6

UniProtKB/TrEMBL

A0A8M9PWY0

Conserved Domains (1) summary

cl02608
Location:101 → 133

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...