mbd3a methyl-CpG binding domain protein 3a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: mbd3aprovided by ZNC
Official Full Name: methyl-CpG binding domain protein 3aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-9077
See related: Ensembl:ENSDARG00000061774 AllianceGenome:ZFIN:ZDB-GENE-030131-9077
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: wu:fa98f07
Summary: Predicted to enable methyl-CpG binding activity. Acts upstream of or within determination of heart left/right asymmetry. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in blastomere and pharyngeal arch 3-7 skeleton. Orthologous to human MBD3 (methyl-CpG binding domain protein 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (57239980..57264312, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (57026758..57051101, complement)

Chromosome 2 - NC_007113.7 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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See details

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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Markers

fe37a07.y1 (e-PCR)
- UniSTS:196411

fa98f07.x1 (e-PCR)
- UniSTS:202628

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within determination of heart left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: methyl-CpG-binding domain protein 3a

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_212769.1 → NP_997934.1 methyl-CpG-binding domain protein 3a

See identical proteins and their annotated locations for NP_997934.1

Status: PROVISIONAL

Source sequence(s)

AY398379

UniProtKB/TrEMBL

A0A8M1PHU0, Q6TGX7

Related

ENSDARP00000082941.4, ENSDART00000088508.6

Conserved Domains (3) summary

cd01396
Location:5 → 78

MeCP2_MBD; MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding ...

pfam14048
Location:152 → 242

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:87 → 147

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

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_007113.7 Reference GRCz11 Primary Assembly

Range

57239980..57264312 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005168451.5 → XP_005168508.1 methyl-CpG-binding domain protein 3a isoform X1

See identical proteins and their annotated locations for XP_005168508.1

UniProtKB/TrEMBL

A0A8M2BFR8, Q7ZTV2

Related

ENSDARP00000154556.1, ENSDART00000183815.1

Conserved Domains (3) summary

pfam14048
Location:120 → 210

MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3

pfam16564
Location:55 → 115

MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

cl00110
Location:5 → 46

MBD; MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to ...