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mbd3.S methyl-CpG binding domain protein 3 S homeolog [ Xenopus laevis (African clawed frog) ]

Gene ID: 398135, updated on 4-Nov-2024

Summary

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Official Symbol
mbd3.S
Official Full Name
methyl-CpG binding domain protein 3 S homeolog
Primary source
Xenbase:XB-GENE-491557
Locus tag
XELAEV_18009729mg
See related
EnsemblRapid:ENSXLAG00005029969 AllianceGenome:Xenbase:XB-GENE-491557
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Xenopus laevis
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus
Also known as
mbd3; xmbd3
Summary
Predicted to enable methyl-CpG binding activity. Predicted to act upstream of or within DNA methylation-dependent heterochromatin formation and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Is expressed in ectoderm; musculoskeletal system; nervous system; and pharyngeal arch. Orthologous to human MBD3 (methyl-CpG binding domain protein 3). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See mbd3.S in Genome Data Viewer
Location:
chromosome: 1S
Exon count:
8
Annotation release Status Assembly Chr Location
101 current Xenopus_laevis_v10.1 (GCF_017654675.1) 1S NC_054372.1 (89039871..89048043)
100 previous assembly Xenopus_laevis_v2 (GCF_001663975.1) 1S NC_030725.1 (83845320..83853600)

Chromosome 1S - NC_054372.1Genomic Context describing neighboring genes Neighboring gene transcription factor 3 S homeolog Neighboring gene cytochrome b-c1 complex subunit 10 Neighboring gene mex-3 RNA binding family member D S homeolog Neighboring gene uncharacterized LOC121399362

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Xenopus MBD3 plays a crucial role in an early stage of development. Iwano H, et al. Dev Biol, 2004 Apr 15. PMID 15063177
  2. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Klein SL, et al. Dev Dyn, 2002 Dec. PMID 12454917
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by Xenbase

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables methyl-CpG binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
methyl-CpG binding domain protein 3 S homeolog
Names
methyl-CpG binding protein MBD3 long form

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_001088477.1 → NP_001081946.1  methyl-CpG binding domain protein 3 S homeolog

    See identical proteins and their annotated locations for NP_001081946.1

    Status: PROVISIONAL

    Source sequence(s)
    AF170347
    UniProtKB/TrEMBL
    Q9PUM8, Q9PUM9
    Conserved Domains (3) summary
    cd01396
    Location:5 → 98
    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:173 → 263
    MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
    pfam16564
    Location:103 → 168
    MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD

RefSeqs of Annotated Genomes: Xenopus laevis Annotation Release 101 details...Open this link in a new tab

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

Reference Xenopus_laevis_v10.1 Primary Assembly

Genomic

  1. NC_054372.1 Reference Xenopus_laevis_v10.1 Primary Assembly

    Range
    89039871..89048043
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_018234268.2 → XP_018089757.1  methyl-CpG binding domain protein 3 S homeolog isoform X2

    UniProtKB/TrEMBL
    A0A8J0TR23, Q9PUM9

  2. XM_018234266.2 → XP_018089755.1  methyl-CpG binding domain protein 3 S homeolog isoform X1

    UniProtKB/TrEMBL
    A0A974I0P5, Q8AYP1, Q9PUM9

  3. XM_018234275.2 → XP_018089764.1  methyl-CpG binding domain protein 3 S homeolog isoform X3

    UniProtKB/TrEMBL
    A0A8J0TJB2, Q9PUM9

  4. XM_018234282.2 → XP_018089771.1  methyl-CpG binding domain protein 3 S homeolog isoform X5

    UniProtKB/TrEMBL
    A0A8J0TRY0, Q9PUM9
    Related
    ENSXLAP00005089597.1, ENSXLAT00005091266.1

  5. XM_018234277.2 → XP_018089766.1  methyl-CpG binding domain protein 3 S homeolog isoform X4

    UniProtKB/TrEMBL
    A0A974I116, Q8AYP2, Q9PUM9
    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:153 → 243
    MBD_C; C-terminal domain of methyl-CpG binding protein 2 and 3
    pfam16564
    Location:83 → 148
    MBDa; p55-binding region of Methyl-CpG-binding domain proteins MBD
Nucleotide Protein Strain
Heading Accession and Version

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