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Kdm3b lysine demethylase 3B [ Rattus norvegicus (Norway rat) ]

Gene ID: 682469, updated on 2-Nov-2024

Summary

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Symbol
Kdm3bprovided by RGD
Full Name
lysine demethylase 3Bprovided by RGD
Primary source
RGD:1583423
See related
EnsemblRapid:ENSRNOG00000050200 AllianceGenome:RGD:1583423
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables antioxidant activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of histone deacetylase complex. Used to study anxiety disorder and visual epilepsy. Orthologous to human KDM3B (lysine demethylase 3B). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 180.5), Spleen (RPKM 143.7) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Kdm3b in Genome Data Viewer
Location:
18p12
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (26655004..26710814)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (26380859..26436701)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (27593823..27631129)

Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC108348765 Neighboring gene stem-loop binding protein like Neighboring gene family with sequence similarity 53, member C Neighboring gene receptor accessory protein 2 Neighboring gene early growth response 1

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. [Olygopeptide KND as a putative endogenous prototype of delta sleep inducing peptide (DSIP). Comparative study of biological properties]. Mikhaleva II, et al. Bioorg Khim, 2013 May-Jun. PMID 24397026
  2. JmjC-domain-containing histone demethylases of the JMJD1B type as putative precursors of endogenous DSIP. Mikhaleva II, et al. Peptides, 2011 Apr. PMID 21262293
  3. DNA profiling by array comparative genomic hybridization (CGH) of peripheral blood mononuclear cells (PBMC) and tumor tissue cell in non-small cell lung cancer (NSCLC). Baik SH, et al. Mol Biol Rep, 2009 Sep. PMID 18975135
  4. An epigenetic role for PRL-3 as a regulator of H3K9 methylation in colorectal cancer. Liu Y, et al. Gut, 2013 Apr. PMID 22345654
  5. KDM3B is the H3K9 demethylase involved in transcriptional activation of lmo2 in leukemia. Kim JY, et al. Mol Cell Biol, 2012 Jul. PMID 22615488, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables antioxidant activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cellular oxidant detoxification IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in demethylation 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 chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
lysine-specific demethylase 3B
Names
lysine (K)-specific demethylase 3B
lysine-specific demethylase 3B-like
NP_001414398.1
XP_038953205.1
XP_038953206.1

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_001427469.1 → NP_001414398.1  lysine-specific demethylase 3B

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000018
    UniProtKB/TrEMBL
    A0A8I5ZXX2, A6J2W3
    Related
    ENSRNOP00000082780.1, ENSRNOT00000110221.2

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_086036.1 Reference GRCr8

    Range
    26655004..26710814
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039097278.2 → XP_038953206.1  lysine-specific demethylase 3B isoform X2

    UniProtKB/TrEMBL
    A0A8I6AC36, M0RDF1
    Related
    ENSRNOP00000090259.1, ENSRNOT00000111068.2
    Conserved Domains (3) summary
    smart00558
    Location:1303 → 1375
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    PRK11901
    Location:473 → 558
    PRK11901; hypothetical protein; Reviewed
    cl40423
    Location:1400 → 1505
    cupin_RmlC-like; RmlC-like cupin superfamily

  2. XM_039097277.2 → XP_038953205.1  lysine-specific demethylase 3B isoform X1

    UniProtKB/TrEMBL
    M0RDF1
    Conserved Domains (2) summary
    smart00558
    Location:1355 → 1427
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl40423
    Location:1452 → 1557
    cupin_RmlC-like; RmlC-like cupin superfamily
Nucleotide Protein Strain
Heading Accession and Version

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