Kdm3 Lysine demethylase 3 [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: Kdm3provided by FlyBase
Official Full Name: Lysine demethylase 3provided by FlyBase
Primary source: FLYBASE:FBgn0037703
Locus tag: Dmel_CG8165
See related: AllianceGenome:FB:FBgn0037703
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: CG31123; CG8165; Dmel\CG8165; JHDM2; kdm3; KDM3
Summary: Enables histone H3K9me/H3K9me2 demethylase activity. Involved in negative regulation of DNA methylation-dependent heterochromatin formation. Located in chromatin. Used to study alcohol use disorder. Human ortholog(s) of this gene implicated in alopecia; alopecia universalis; atrichia with papular lesions; cervical cancer; and colon cancer. Orthologous to several human genes including KDM3A (lysine demethylase 3A) and KDM3B (lysine demethylase 3B). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 85D19-85D19; 3-48 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3R	NT_033777.3 (9516007..9520938)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3R	NT_033777.2 (5341729..5346660)

Chromosome 3R - NT_033777.3 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?

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.
Paper describes the multifunctional cupin superfamily. This protein contains the cupin signature at its C-terminus. Residues H643, D645, and H774 represent the conserved Fe binding ligands of the active site of this presumed dioxygenase subtype.
Title: Evolution of functional diversity in the cupin superfamily.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

mir-2283-RA; Dmel\mir-2283-RA; CR42887-RA; Dmel\CR42887-RA

mir-2283-RB; Dmel\mir-2283-RB; CR42887-RB; Dmel\CR42887-RB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9me/H3K9me2 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9me/H3K9me2 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in negative regulation of heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISM Inferred from Sequence Model more info	PubMed

General protein information

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Preferred Names: lysine demethylase 3

Names: CG8165-PA; CG8165-PB; JmjC domain-containing histone demethylase 2; Kdm3-PA; Kdm3-PB

NP_001287255.1

EC 1.14.11.65

NP_788611.1

EC 1.14.11.65

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_033777.3 Reference assembly

Range

9516007..9520938

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_176434.2 → NP_788611.1 lysine demethylase 3, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_788611.1

Status: REVIEWED

UniProtKB/TrEMBL

Q9VHC5

Related

FBpp0081541

Conserved Domains (2) summary

smart00558
Location:605 → 657

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cl21464
Location:694 → 789

cupin_like; Conserved domain found in cupin and related proteins
NM_001300326.1 → NP_001287255.1 lysine demethylase 3, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001287255.1

Status: REVIEWED

UniProtKB/TrEMBL

Q9VHC5

Conserved Domains (2) summary

smart00558
Location:605 → 657

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cl21464
Location:694 → 789

cupin_like; Conserved domain found in cupin and related proteins