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

    Gene ID: 33837, updated on 2-Nov-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, Nov 2024]
    Orthologs
    all
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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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