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Gatad2b GATA zinc finger domain containing 2B [ Rattus norvegicus (Norway rat) ]

Gene ID: 310614, updated on 10-Oct-2024

Summary

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Official Symbol
Gatad2bprovided by RGD
Official Full Name
GATA zinc finger domain containing 2Bprovided by RGD
Primary source
RGD:1308533
See related
EnsemblRapid:ENSRNOG00000015553 AllianceGenome:RGD:1308533
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1308533
Summary
Predicted to enable sequence-specific DNA binding activity and zinc ion binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of NuRD complex. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability 18. Orthologous to human GATAD2B (GATA zinc finger domain containing 2B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 117.7), Spleen (RPKM 105.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Gatad2b in Genome Data Viewer
Location:
2q34
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (178046192..178127633)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (175748594..175829837)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (189654871..189735056)

Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene CREB regulated transcription coactivator 2 Neighboring gene uncharacterized LOC102551157 Neighboring gene DENN domain containing 4B Neighboring gene solute carrier family 27 member 3 Neighboring gene integrator complex subunit 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. The nucleosome remodeling and deacetylase complex in development and disease. Basta J, et al. Transl Res, 2015 Jan. PMID 24880148, Free PMC Article
  2. Heterogeneous nuclear ribonucleoprotein C1/C2, MeCP1, and SWI/SNF form a chromatin remodeling complex at the beta-globin locus control region. Mahajan MC, et al. Proc Natl Acad Sci U S A, 2005 Oct 18. PMID 16217013, Free PMC Article
  3. p38α MAPK proximity assay reveals a regulatory mechanism of alternative splicing in cardiomyocytes. Dumont AA, et al. Biochim Biophys Acta Mol Cell Res, 2019 Dec. PMID 31505169
  4. 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
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of NuRD complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of NuRD complex ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
transcriptional repressor p66-beta
Names
transcription repressor p66 beta component of the MeCP1 complex

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_001024888.1 → NP_001020059.1  transcriptional repressor p66-beta

    See identical proteins and their annotated locations for NP_001020059.1

    Status: PROVISIONAL

    Source sequence(s)
    BC097428
    UniProtKB/TrEMBL
    A6J6L7, Q4V8E1
    Related
    ENSRNOP00000091300.2, ENSRNOT00000117370.2
    Conserved Domains (2) summary
    pfam00320
    Location:420 → 454
    GATA; GATA zinc finger
    pfam16563
    Location:159 → 194
    P66_CC; Coiled-coil and interaction region of P66A and P66B with MBD2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086020.1 Reference GRCr8

    Range
    178046192..178127633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039102301.2 → XP_038958229.1  transcriptional repressor p66-beta isoform X1

    UniProtKB/TrEMBL
    A0A8I6AFB3, A6J6L7
    Related
    ENSRNOP00000071152.3, ENSRNOT00000086285.3

  2. XM_039102302.2 → XP_038958230.1  transcriptional repressor p66-beta isoform X2

    UniProtKB/TrEMBL
    A6J6L7

  3. XM_008761144.4 → XP_008759366.1  transcriptional repressor p66-beta isoform X3

    See identical proteins and their annotated locations for XP_008759366.1

    UniProtKB/TrEMBL
    A6J6L7, Q4V8E1
    Conserved Domains (2) summary
    pfam00320
    Location:420 → 454
    GATA; GATA zinc finger
    pfam16563
    Location:159 → 194
    P66_CC; Coiled-coil and interaction region of P66A and P66B with MBD2

  4. XM_063281824.1 → XP_063137894.1  transcriptional repressor p66-beta isoform X4

  5. XM_063281823.1 → XP_063137893.1  transcriptional repressor p66-beta isoform X3

    UniProtKB/TrEMBL
    Q4V8E1
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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