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Kdm5 Lysine demethylase 5 [ Drosophila melanogaster (fruit fly) ]

Gene ID: 33837, updated on 9-Dec-2024

Summary

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Official Symbol
Kdm5provided by FlyBase
Official Full Name
Lysine demethylase 5provided by FlyBase
Primary source
FLYBASE:FBgn0031759
Locus tag
Dmel_CG9088
See related
AllianceGenome:FB:FBgn0031759
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Drosophila melanogaster
Lineage
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as
CG9088; dJARID1; dKDM5; dKDM5/LID; Dmel\CG9088; kdm5; KDM5; l(2)10424; lid; Lid; LID; Lid/KDM5
Summary
Enables enzyme inhibitor activity; histone demethylase activity; and histone reader activity. Involved in several processes, including chromosome organization; larval somatic muscle development; and regulation of gene expression. Located in nucleus. Part of Sin3-type complex. Is expressed in several structures, including adult pars intercerebralis; brain; larval ventral nerve cord; oocyte; and testis. Used to study alcohol use disorder; autism spectrum disorder; intellectual disability; syndromic X-linked intellectual disability Claes-Jensen type; and syndromic intellectual disability. Human ortholog(s) of this gene implicated in ankylosing spondylitis; breast cancer; descending colon cancer; high grade glioma; and intellectual disability (multiple). Orthologous to several human genes including KDM5A (lysine demethylase 5A); KDM5B (lysine demethylase 5B); and KDM5C (lysine demethylase 5C). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs
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Genomic context

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See Kdm5 in Genome Data Viewer
Location:
26B2-26B2; 2-18 cM
Exon count:
7
Annotation release Status Assembly Chr Location
Release 6.54 current Release 6 plus ISO1 MT (GCF_000001215.4) 2L NT_033779.5 (5989400..5999501, complement)
Release 5.57 previous assembly Release 5 (GCF_000001215.2) 2L NT_033779.4 (5989400..5999501, complement)

Chromosome 2L - NT_033779.5Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4A Neighboring gene infertile crescent Neighboring gene Tetraspanin 26A Neighboring gene antisense RNA:CR43866 Neighboring gene beta galactosidase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction. Belalcazar HM, et al. Cell Rep, 2021 Feb 16. PMID 33596422, Free PMC Article
  2. A Drosophila Model of Intellectual Disability Caused by Mutations in the Histone Demethylase KDM5. Zamurrad S, et al. Cell Rep, 2018 Feb 27. PMID 29490272, Free PMC Article
  3. KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Yheskel M, et al. Nucleic Acids Res, 2024 Jun 24. PMID 38597673, Free PMC Article
  4. Lysine-specific histone demethylase LSD1 and the dynamic control of chromatin. Rudolph T, et al. Biol Chem, 2013 Aug. PMID 23612539
  5. Drosophila Model for Studying Gut Microbiota in Behaviors and Neurodegenerative Diseases. Chiang MH, et al. Biomedicines, 2022 Mar 3. PMID 35327401, Free PMC Article

See all (153) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila.
    Title: KDM5-mediated activation of genes required for mitochondrial biology is necessary for viability in Drosophila.
  2. BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels.
    Title: BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels.
  3. Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5.
    Title: Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5.
  4. The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction.
    Title: The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction.
  5. KDM5 functions by promoting the endoreplication of prothoracic gland cells, a process that increases ploidy and is rate limiting for the expression of ecdysone biosynthetic genes. KDM5 activates the expression of the receptor tyrosine kinase torso, which then promotes polyploidization and growth through activation of the MAPK signaling pathway.
    Title: The histone demethylase KDM5 controls developmental timing in Drosophila by promoting prothoracic gland endocycles.
  6. Reducing KDM5 causes intestinal barrier dysfunction and changes in social behavior that correlates with compositional changes in the gut microbiota.
    Title: Drosophila Histone Demethylase KDM5 Regulates Social Behavior through Immune Control and Gut Microbiota Maintenance.
  7. the primary defect of the KDM5(A512P) mutation is a loss of histone demethylase activity and reveal an unexpected role for this enzymatic function in gene activation.
    Title: A Drosophila Model of Intellectual Disability Caused by Mutations in the Histone Demethylase KDM5.
  8. However, for the N terminal region harboring both a PHD and an ARID finger, Lid anchors to the NuMat via both protein-protein and protein-DNA interactions. The association of JmjC domain with NuMat is the first report of the association of a demethylase domain with NuMat suggesting that Lid, a demethylase, being part of NuMat might be involved in regulating the chromatin dynamics via its NuMat association.
    Title: Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos.
  9. Analyses reveal KDM5 as a key regulator of larval growth and offer an invaluable tool for defining the biological activities of KDM5 family proteins.
    Title: The Histone Demethylase KDM5 Is Essential for Larval Growth in Drosophila.
  10. Therefore Kdm5/Lid controls chromatin architecture in meiotic prophase I oocytes independently of its demethylase activity.
    Title: Kdm5/Lid Regulates Chromosome Architecture in Meiotic Prophase I Independently of Its Histone Demethylase Activity.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by FlyBase

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables enzyme inhibitor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H4R3 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone reader activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in circadian regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in larval somatic muscle development IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in larval somatic muscle development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in locomotor rhythm IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in male germ-line stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in oocyte karyosome formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptonemal complex organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Sin3-type complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
lysine demethylase 5
Names
CG9088-PA
CG9088-PB
CG9088-PC
CG9088-PD
CG9088-PE
CG9088-PF
Kdm5-PA
Kdm5-PB
Kdm5-PC
Kdm5-PD
Kdm5-PE
Kdm5-PF
little imaginal discs
little imaginal disks
NP_001245908.1
NP_001245909.1
NP_001245910.1
NP_001285649.1
NP_523486.1
NP_723140.1

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

  1. NT_033779.5 Reference assembly

    Range
    5989400..5999501 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001298720.1 → NP_001285649.1  lysine demethylase 5, isoform F [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_001285649.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9VMJ7
    UniProtKB/TrEMBL
    M9NEV0
    Conserved Domains (8) summary
    smart00545
    Location:160 → 201
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:227 → 312
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:624 → 740
    JmjC; JmjC domain, hydroxylase
    cd15605
    Location:450 → 495
    PHD1_Lid_like; PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins
    cd15606
    Location:1295 → 1351
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15610
    Location:1755 → 1805
    PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins
    pfam02928
    Location:830 → 882
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:896 → 1229
    PLU-1; PLU-1-like protein

  2. NM_001258981.2 → NP_001245910.1  lysine demethylase 5, isoform E [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_001245910.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9VMJ7
    UniProtKB/TrEMBL
    M9NEV0
    Conserved Domains (8) summary
    smart00545
    Location:160 → 201
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:227 → 312
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:624 → 740
    JmjC; JmjC domain, hydroxylase
    cd15605
    Location:450 → 495
    PHD1_Lid_like; PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins
    cd15606
    Location:1295 → 1351
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15610
    Location:1755 → 1805
    PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins
    pfam02928
    Location:830 → 882
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:896 → 1229
    PLU-1; PLU-1-like protein

  3. NM_001258979.2 → NP_001245908.1  lysine demethylase 5, isoform C [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_001245908.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9VMJ7
    UniProtKB/TrEMBL
    M9NEV0
    Conserved Domains (8) summary
    smart00545
    Location:160 → 201
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:227 → 312
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:624 → 740
    JmjC; JmjC domain, hydroxylase
    cd15605
    Location:450 → 495
    PHD1_Lid_like; PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins
    cd15606
    Location:1295 → 1351
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15610
    Location:1755 → 1805
    PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins
    pfam02928
    Location:830 → 882
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:896 → 1229
    PLU-1; PLU-1-like protein

  4. NM_078762.6 → NP_523486.1  lysine demethylase 5, isoform A [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_523486.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9VMJ7
    UniProtKB/TrEMBL
    M9NEV0
    Related
    FBpp0078862
    Conserved Domains (8) summary
    smart00545
    Location:160 → 201
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:227 → 312
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:624 → 740
    JmjC; JmjC domain, hydroxylase
    cd15605
    Location:450 → 495
    PHD1_Lid_like; PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins
    cd15606
    Location:1295 → 1351
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15610
    Location:1755 → 1805
    PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins
    pfam02928
    Location:830 → 882
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:896 → 1229
    PLU-1; PLU-1-like protein

  5. NM_001258980.1 → NP_001245909.1  lysine demethylase 5, isoform D [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_001245909.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9VMJ7
    UniProtKB/TrEMBL
    M9NEV0
    Conserved Domains (8) summary
    smart00545
    Location:160 → 201
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:227 → 312
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:624 → 740
    JmjC; JmjC domain, hydroxylase
    cd15605
    Location:450 → 495
    PHD1_Lid_like; PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins
    cd15606
    Location:1295 → 1351
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15610
    Location:1755 → 1805
    PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins
    pfam02928
    Location:830 → 882
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:896 → 1229
    PLU-1; PLU-1-like protein

  6. NM_164671.1 → NP_723140.1  lysine demethylase 5, isoform B [Drosophila melanogaster]

    See identical proteins and their annotated locations for NP_723140.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    Q9VMJ7
    UniProtKB/TrEMBL
    M9NEV0
    Related
    FBpp0078863, FBtr0079232
    Conserved Domains (8) summary
    smart00545
    Location:160 → 201
    JmjN; Small domain found in the jumonji family of transcription factors
    smart01014
    Location:227 → 312
    ARID; ARID/BRIGHT DNA binding domain
    pfam02373
    Location:624 → 740
    JmjC; JmjC domain, hydroxylase
    cd15605
    Location:450 → 495
    PHD1_Lid_like; PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins
    cd15606
    Location:1295 → 1351
    PHD2_KDM5A; PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A)
    cd15610
    Location:1755 → 1805
    PHD3_KDM5A_like; PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins
    pfam02928
    Location:830 → 882
    zf-C5HC2; C5HC2 zinc finger
    pfam08429
    Location:896 → 1229
    PLU-1; PLU-1-like protein
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
M9NEV0 M9NEV0
Q9VMJ7.1 Q9VMJ7

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