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

Summary

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, Jul 2025]
Orthologs: all
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Genomic context

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_033779.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels.
Title: BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels.
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.
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.
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.
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.
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.
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.
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.
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

Dm0352 (e-PCR)
- UniSTS:29812

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables enzyme inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation 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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of behavioral response to ethanol	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
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 behavior	IMP Inferred from Mutant Phenotype more info	PubMed
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 regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation 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
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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
located_in nucleus	IEA Inferred from Electronic Annotation more info

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

EC 1.14.11.67

NP_001245909.1

EC 1.14.11.67

NP_001245910.1

EC 1.14.11.67

NP_001285649.1

EC 1.14.11.67

NP_523486.1

EC 1.14.11.67

NP_723140.1

EC 1.14.11.67

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

NT_033779.5 Reference assembly

Range

5989400..5999501 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001298720.1 → NP_001285649.1 lysine demethylase 5, isoform F

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
NM_001258981.2 → NP_001245910.1 lysine demethylase 5, isoform E

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
NM_001258979.2 → NP_001245908.1 lysine demethylase 5, isoform C

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
NM_078762.6 → NP_523486.1 lysine demethylase 5, isoform A

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
NM_001258980.1 → NP_001245909.1 lysine demethylase 5, isoform D

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
NM_164671.1 → NP_723140.1 lysine demethylase 5, isoform B

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