jmjd-2 Lysine-specific demethylase 4 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: jmjd-2
Official Full Name: Lysine-specific demethylase 4
Primary source: WormBase:WBGene00012982
Locus tag: CELE_Y48B6A.11
See related: AllianceGenome:WB:WBGene00012982
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables histone H3K36me/H3K36me2 demethylase activity and histone H3K9me2/H3K9me3 demethylase activity. Predicted to be involved in chromatin remodeling and negative regulation of DNA-templated transcription. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in pharynx. Human ortholog(s) of this gene implicated in several diseases, including autistic disorder; gastrointestinal system cancer (multiple); head and neck cancer; malignant peripheral nerve sheath tumor; and withdrawal disorder. Orthologous to several human genes including KDM4C (lysine demethylase 4C). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See jmjd-2 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 6

Sequence:: Chromosome: II; NC_003280.10 (14234979..14243603, complement)

Chromosome II - NC_003280.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003280.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

targeting of the Jumonji demethylases JMJD-2 and JMJD-3/UTX-1 restores H3K9me3 and H3K27me3 levels, respectively, and it fully alleviates the bisphenol A-induced transgenerational effects
Title: The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1.

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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

Y48B6A.11 (e-PCR)
- UniSTS:321747

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables 2-oxoglutarate-dependent dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K36me/H3K36me2 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K36me2/H3K36me3 demethylase activity	IEA Inferred from Electronic Annotation 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 H3K9me2/H3K9me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9me2/H3K9me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of gene expression	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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: Lysine-specific demethylase 4

NP_496969.2

Confirmed by transcript evidence

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

NC_003280.10 Reference assembly

Range

14234979..14243603 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_064568.6 → NP_496969.2 Lysine-specific demethylase 4 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_496969.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9U297

Conserved Domains (4) summary

smart00545
Location:86 → 129

JmjN; Small domain found in the jumonji family of transcription factors

pfam02373
Location:252 → 371

JmjC; JmjC domain, hydroxylase

cd15571
Location:642 → 782

ePHD; Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His

cl22851
Location:588 → 629

PHD_SF; PHD finger superfamily