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    KDM7A lysine demethylase 7A [ Homo sapiens (human) ]

    Gene ID: 80853, updated on 10-Dec-2024

    Summary

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    Official Symbol
    KDM7Aprovided by HGNC
    Official Full Name
    lysine demethylase 7Aprovided by HGNC
    Primary source
    HGNC:HGNC:22224
    See related
    Ensembl:ENSG00000006459 MIM:619640; AllianceGenome:HGNC:22224
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    JHDM1D
    Summary
    Enables histone demethylase activity; methylated histone binding activity; and transition metal ion binding activity. Predicted to be involved in midbrain development and regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Implicated in melanoma. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 9.6), colon (RPKM 7.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KDM7A in Genome Data Viewer
    Location:
    7q34
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (140084746..140176983, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (141398329..141490536, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (139784546..139876783, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18701 Neighboring gene poly(ADP-ribose) polymerase family member 12 Neighboring gene MPRA-validated peak6786 silencer Neighboring gene MPRA-validated peak6788 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26773 Neighboring gene uncharacterized LOC124901757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:139825166-139825666 Neighboring gene Sharpr-MPRA regulatory region 991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18704 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:139876416-139877339 Neighboring gene KDM7A divergent transcript Neighboring gene RNA, U6 small nuclear 797, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. JHDM1D-AS1 aggravates the development of gastric cancer through miR-450a-2-3p-PRAF2 axis. Wu M, et al. Life Sci, 2021 Jan 15. PMID 33245963
    2. The nuclear bodies formed by histone demethylase KDM7A. Ming H, et al. Protein Cell, 2021 Apr. PMID 32935279, Free PMC Article
    3. Histone demethylase KDM7A is required for stem cell maintenance and apoptosis inhibition in breast cancer. Meng Z, et al. J Cell Physiol, 2020 Feb. PMID 31236965
    4. Histone demethylase KDM7A controls androgen receptor activity and tumor growth in prostate cancer. Lee KH, et al. Int J Cancer, 2018 Dec 1. PMID 30183076
    5. Decreased expression of JHDMID in placenta is associated with preeclampsia through HLA-G. Luo S, et al. J Hum Hypertens, 2018 Jun. PMID 29662139

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Inhibition of KDM2/7 Promotes Notochordal Differentiation of hiPSCs.
      Title: Inhibition of KDM2/7 Promotes Notochordal Differentiation of hiPSCs.
    2. The nuclear bodies formed by histone demethylase KDM7A.
      Title: The nuclear bodies formed by histone demethylase KDM7A.
    3. Histone Demethylase KDM7A Regulates Androgen Receptor Activity, and Its Chemical Inhibitor TC-E 5002 Overcomes Cisplatin-Resistance in Bladder Cancer Cells.
      Title: Histone Demethylase KDM7A Regulates Androgen Receptor Activity, and Its Chemical Inhibitor TC-E 5002 Overcomes Cisplatin-Resistance in Bladder Cancer Cells.
    4. JHDM1D-AS1 aggravates the development of gastric cancer through miR-450a-2-3p-PRAF2 axis.
      Title: JHDM1D-AS1 aggravates the development of gastric cancer through miR-450a-2-3p-PRAF2 axis.
    5. Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells.
      Title: Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells.
    6. Histone demethylase KDM7A is required for stem cell maintenance and apoptosis inhibition in breast cancer.
      Title: Histone demethylase KDM7A is required for stem cell maintenance and apoptosis inhibition in breast cancer.
    7. decreased expression in placenta associated with pre-eclampsia through down-regulating HLA-G
      Title: Decreased expression of JHDMID in placenta is associated with preeclampsia through HLA-G.
    8. KDM7A is potentially a good therapeutic target for prostate cancer drugs.
      Title: Histone demethylase KDM7A controls androgen receptor activity and tumor growth in prostate cancer.
    9. KDM7A mediates TNF-alpha-induced ICAM1 protein upregulation.
      Title: KDM7A histone demethylase mediates TNF-α-induced ICAM1 protein upregulation by modulating lysosomal activity.
    10. G9a promotes H3K27 methylation of the E-cadherin promoter by upregulating PCL3 to increase PRC2 promoter recruitment and by downregulating the H3K27 demethylase KDM7A to silence E-cadherin gene
      Title: G9a orchestrates PCL3 and KDM7A to promote histone H3K27 methylation.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of jumonji C domain containing histone demethylase 1 homolog D (JHDM1D) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1718

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K36 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9me/H3K9me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K20 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
    		  
    enables iron ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables iron ion binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in midbrain development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of DNA-templated transcription 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 nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysine-specific demethylase 7A
    Names
    [histone H3]-dimethyl-L-lysine9 demethylase 7A
    histone lysine demethylase JHDM1D
    jmjC domain-containing histone demethylation protein 1D
    jumonji C domain containing histone demethylase 1 homolog D
    lysine (K)-specific demethylase 7A
    lysine-specific demethylase 7
    NP_085150.1
    XP_011514889.1
    XP_047276835.1
    XP_054215057.1
    XP_054215058.1

    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_030647.2 → NP_085150.1  lysine-specific demethylase 7A

      See identical proteins and their annotated locations for NP_085150.1

      Status: VALIDATED

      Source sequence(s)
      AB051505, AC004849, AK131497
      Consensus CDS
      CCDS43658.1
      UniProtKB/Swiss-Prot
      A4D1S9, C9JJH9, C9JQU2, Q6MZL8, Q6ZMT4, Q9C0E5
      Related
      ENSP00000380692.2, ENST00000397560.7
      Conserved Domains (3) summary
      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)
      cl21464
      Location:269 → 369
      cupin_like; Conserved domain found in cupin and related proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      140084746..140176983 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011516587.3 → XP_011514889.1  lysine-specific demethylase 7A isoform X2

      See identical proteins and their annotated locations for XP_011514889.1

    2. XM_047420879.1 → XP_047276835.1  lysine-specific demethylase 7A isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      141398329..141490536 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359083.1 → XP_054215058.1  lysine-specific demethylase 7A isoform X2

    2. XM_054359082.1 → XP_054215057.1  lysine-specific demethylase 7A isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZMT4.2 GenPept UniProtKB/Swiss-Prot:Q6ZMT4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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