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

    Gene ID: 682469, updated on 9-Dec-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, Dec 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
    • 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 dioxygenase activity IEA
    Inferred from Electronic Annotation
    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, M0RDF1
      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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