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    kdm2aa lysine (K)-specific demethylase 2Aa [ Danio rerio (zebrafish) ]

    Gene ID: 571851, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm2aaprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 2Aaprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-061215-144
    See related
    Ensembl:ENSDARG00000059653 AllianceGenome:ZFIN:ZDB-GENE-061215-144
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    jhdm1A-b; wu:fb76b11; wu:fj11c04; zgc:158441; zgc:158606
    Summary
    Predicted to enable histone demethylase activity and transcription coregulator activity. Acts upstream of or within sex determination. Predicted to be located in nucleus. Used to study melanoma. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human KDM2A (lysine demethylase 2A). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kdm2aa in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (44838706..44869972)
    105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (44137403..44168669)

    Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase core subunit S8a Neighboring gene syntaxin 3a Neighboring gene T cell immune regulator 1, ATPase H+ transporting V0 subunit a3a Neighboring gene wu:fc21g02 Neighboring gene si:dkey-9i23.15

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish. Scahill CM, et al. PLoS Genet, 2017 Aug. PMID 28806732, Free PMC Article
    2. KDM2A integrates DNA and histone modification signals through a CXXC/PHD module and direct interaction with HP1. Borgel J, et al. Nucleic Acids Res, 2017 Feb 17. PMID 28180290, Free PMC Article
    3. Molecular characterization of the zebrafish P2X receptor subunit gene family. Kucenas S, et al. Neuroscience, 2003. PMID 14580944
    4. The histone demethylase Jmjd3 regulates zebrafish myeloid development by promoting spi1 expression. Yu SH, et al. Biochim Biophys Acta Gene Regul Mech, 2018 Feb. PMID 29378332, Free PMC Article
    5. Characterization of the Apelin/Elabela Receptors (APLNR) in Chickens, Turtles, and Zebrafish: Identification of a Novel Apelin-Specific Receptor in Teleosts. Zhang J, et al. Front Endocrinol (Lausanne), 2018. PMID 30631305, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. loss of the orthologue kdm2aa in zebrafish causes widespread transcriptional disruption and leads to spontaneous melanomas at a high frequency
      Title: Loss of the chromatin modifier Kdm2aa causes BrafV600E-independent spontaneous melanoma in zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC158441

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K36me/H3K36me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within sex determination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine (K)-specific demethylase 2Aa
    Names
    JmjC domain-containing histone demethylation protein 1B
    NP_001075161.2
    XP_005160305.1
    XP_009291632.1
    XP_009291637.1
    XP_009291640.1

    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_001081692.2 → NP_001075161.2  lysine (K)-specific demethylase 2Aa

      Status: VALIDATED

      Source sequence(s)
      BX901937
      UniProtKB/TrEMBL
      A0A0R4IH56, A0A8M1NBS2
      Related
      ENSDARP00000134050.1, ENSDART00000162779.2
      Conserved Domains (6) summary
      cd09293
      Location:1093 → 1268
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:511 → 545
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:1067 → 1091
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam12937
      Location:1033 → 1073
      F-box-like; F-box-like
      pfam16866
      Location:550 → 606
      PHD_4; PHD-finger
      cl21464
      Location:199 → 299
      cupin_like; Conserved domain found in cupin and related proteins

    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

    1. NC_007112.7 Reference GRCz11 Primary Assembly

      Range
      44838706..44869972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009293357.4 → XP_009291632.1  lysine (K)-specific demethylase 2Aa isoform X2

      UniProtKB/TrEMBL
      A0A8M3B2Q2
      Conserved Domains (6) summary
      cd09293
      Location:1091 → 1266
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:509 → 543
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:1065 → 1089
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam12937
      Location:1031 → 1071
      F-box-like; F-box-like
      pfam16866
      Location:548 → 604
      PHD_4; PHD-finger
      cl21464
      Location:197 → 297
      cupin_like; Conserved domain found in cupin and related proteins

    2. XM_009293365.4 → XP_009291640.1  lysine (K)-specific demethylase 2Aa isoform X4

      UniProtKB/TrEMBL
      A0A8M3AJC4
      Conserved Domains (6) summary
      cd09293
      Location:1037 → 1212
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:455 → 489
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:1011 → 1035
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam12937
      Location:977 → 1017
      F-box-like; F-box-like
      pfam16866
      Location:494 → 550
      PHD_4; PHD-finger
      cl21464
      Location:143 → 243
      cupin_like; Conserved domain found in cupin and related proteins

    3. XM_005160248.5 → XP_005160305.1  lysine (K)-specific demethylase 2Aa isoform X1

      UniProtKB/TrEMBL
      A0A8M2B724
      Conserved Domains (6) summary
      cd09293
      Location:1116 → 1291
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:534 → 568
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:1090 → 1114
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam12937
      Location:1056 → 1096
      F-box-like; F-box-like
      pfam16866
      Location:573 → 629
      PHD_4; PHD-finger
      cl21464
      Location:222 → 322
      cupin_like; Conserved domain found in cupin and related proteins

    4. XM_009293362.4 → XP_009291637.1  lysine (K)-specific demethylase 2Aa isoform X3

      UniProtKB/TrEMBL
      A0A8M3AK71
      Conserved Domains (6) summary
      cd09293
      Location:1063 → 1238
      AMN1; Antagonist of mitotic exit network protein 1
      pfam02008
      Location:534 → 568
      zf-CXXC; CXXC zinc finger domain
      sd00034
      Location:1037 → 1061
      LRR_AMN1; leucine-rich repeat [structural motif]
      pfam12937
      Location:1003 → 1043
      F-box-like; F-box-like
      pfam16866
      Location:573 → 629
      PHD_4; PHD-finger
      cl21464
      Location:222 → 322
      cupin_like; Conserved domain found in cupin and related proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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