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

Gene ID: 571851, updated on 27-Mar-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, Apr 2022]
Orthologs
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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
106 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 (10) 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 histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
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
  
involved_in protein demethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
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; lysine (K)-specific demethylase 2B
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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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_009293357.3 → XP_009291632.1  lysine (K)-specific demethylase 2B 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_005160248.4 → XP_005160305.1  lysine (K)-specific demethylase 2B 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

  3. XM_009293362.3 → XP_009291637.1  lysine (K)-specific demethylase 2B 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

  4. XM_009293365.3 → XP_009291640.1  lysine (K)-specific demethylase 2B 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
Nucleotide Protein Strain
Heading Accession and Version

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