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    Kdm7a lysine demethylase 7A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 684297, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Kdm7aprovided by RGD
    Official Full Name
    lysine demethylase 7Aprovided by RGD
    Primary source
    RGD:1592650
    See related
    Ensembl:ENSRNOG00000052445 AllianceGenome:RGD:1592650
    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
    Also known as
    Jhdm1d
    Summary
    Predicted to enable histone demethylase activity; methylated histone binding activity; and transition metal ion binding activity. Predicted to be involved in histone lysine demethylation and positive regulation of transcription, DNA-templated. Predicted to be located in nucleolus and nucleoplasm. Human ortholog(s) of this gene implicated in melanoma. Orthologous to human KDM7A (lysine demethylase 7A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 187.9), Spleen (RPKM 150.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    4q23
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (68866263..68992979, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (67899407..67974264, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (66915603..66957971, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene thromboxane A synthase 1 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene poly (ADP-ribose) polymerase family, member 12 Neighboring gene uncharacterized LOC134486573 Neighboring gene RNA, U6 small nuclear 604 Neighboring gene chromatin modifying protein 4B-like 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. Increased expression of histone demethylase JHDM1D under nutrient starvation suppresses tumor growth via down-regulating angiogenesis. Osawa T, et al. Proc Natl Acad Sci U S A, 2011 Dec 20. PMID 22143793, Free PMC Article
    2. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Horton JR, et al. Nat Struct Mol Biol, 2010 Jan. PMID 20023638, Free PMC Article
    3. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. Tsukada Y, et al. Genes Dev, 2010 Mar 1. PMID 20194436, Free PMC Article
    4. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Qi HH, et al. Nature, 2010 Jul 22. PMID 20622853, Free PMC Article
    5. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, et al. Mol Cell, 2012 Nov 30. PMID 23200123, Free PMC Article

    See all (6) 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 2-oxoglutarate-dependent dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K27me2/H3K27me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K9 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H4K20 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables iron ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine demethylase 7A; lysine-specific demethylase 7A
    Names
    jumonji C domain containing histone demethylase 1
    lysine (K)-specific demethylase 7A

    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_001428919.1 → NP_001415848.1  lysine demethylase 7A

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004

    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_086022.1 Reference GRCr8

      Range
      68866263..68992979 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063286832.1 → XP_063142902.1  lysine-specific demethylase 7A isoform X1

      UniProtKB/TrEMBL
      A0A8I6AQU2

    2. XM_063286833.1 → XP_063142903.1  lysine-specific demethylase 7A isoform X2

    3. XM_063286827.1 → XP_063142897.1  lysine-specific demethylase 7A isoform X1

      UniProtKB/TrEMBL
      A0A8I6AQU2

    4. XM_063286830.1 → XP_063142900.1  lysine-specific demethylase 7A isoform X1

      UniProtKB/TrEMBL
      A0A8I6AQU2

    5. XM_063286828.1 → XP_063142898.1  lysine-specific demethylase 7A isoform X1

      UniProtKB/TrEMBL
      A0A8I6AQU2

    6. XM_063286831.1 → XP_063142901.1  lysine-specific demethylase 7A isoform X1

      UniProtKB/TrEMBL
      A0A8I6AQU2

    7. XM_039109016.2 → XP_038964944.1  lysine-specific demethylase 7A isoform X1

      UniProtKB/TrEMBL
      A0A0G2K1Z1, A0A8I6AQU2
      Related
      ENSRNOP00000096667.1
      Conserved Domains (5) summary
      TIGR00934
      Location:508 → 823
      2a38euk; potassium uptake protein, Trk family
      smart00558
      Location:234 → 297
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15640
      Location:39 → 88
      PHD_KDM7; PHD finger found in lysine-specific demethylase 7 (KDM7)
      pfam17811
      Location:373 → 476
      JHD; Jumonji helical domain
      cl40423
      Location:269 → 369
      cupin_RmlC-like; RmlC-like cupin superfamily

    8. XM_039109018.2 → XP_038964946.1  lysine-specific demethylase 7A isoform X2

      UniProtKB/TrEMBL
      A0A0G2K1Z1
      Conserved Domains (4) summary
      TIGR00934
      Location:415 → 730
      2a38euk; potassium uptake protein, Trk family
      smart00558
      Location:141 → 204
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam17811
      Location:280 → 383
      JHD; Jumonji helical domain
      cl40423
      Location:176 → 276
      cupin_RmlC-like; RmlC-like cupin superfamily

    9. XM_039109019.2 → XP_038964947.1  lysine-specific demethylase 7A isoform X3

      Conserved Domains (4) summary
      TIGR00934
      Location:304 → 619
      2a38euk; potassium uptake protein, Trk family
      smart00558
      Location:30 → 93
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam17811
      Location:169 → 272
      JHD; Jumonji helical domain
      cl40423
      Location:65 → 165
      cupin_RmlC-like; RmlC-like cupin superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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