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

Gene ID: 80853, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 9.6), colon (RPKM 7.1) and 25 other tissues See more
Orthologs
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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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 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. The nuclear bodies formed by histone demethylase KDM7A.
    Title: The nuclear bodies formed by histone demethylase KDM7A.
  2. Hsa_circ_002178 Promotes the Growth and Migration of Breast Cancer Cells and Maintains Cancer Stem-like Cell Properties Through Regulating miR-1258/KDM7A Axis.
    Title: Hsa_circ_002178 Promotes the Growth and Migration of Breast Cancer Cells and Maintains Cancer Stem-like Cell Properties Through Regulating miR-1258/KDM7A Axis.
  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)

Genotypes

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 chromatin remodeling IEA
Inferred from Electronic Annotation
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.

Chemical Information
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