Kdm4d lysine demethylase 4D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm4dprovided by RGD
Official Full Name: lysine demethylase 4Dprovided by RGD
Primary source: RGD:1591045
See related: EnsemblRapid:ENSRNOG00000045905 AllianceGenome:RGD:1591045
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable chromatin DNA binding activity; damaged DNA binding activity; and histone H3K9me2/H3K9me3 demethylase activity. Predicted to be involved in chromatin remodeling; inflammatory response; and regulation of gene expression. Predicted to act upstream of or within several processes, including cellular response to ionizing radiation; double-strand break repair via homologous recombination; and positive regulation of double-strand break repair via nonhomologous end joining. Predicted to be located in pericentric heterochromatin and site of double-strand break. Predicted to be active in nucleus. Orthologous to human KDM4D (lysine demethylase 4D). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: 8q12

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (19561253..19586412, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (11279756..11304920, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (12968192..12993651, complement)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

RH138188 (e-PCR)
- UniSTS:220275

RH143162 (e-PCR)
- UniSTS:232409

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K9me2/H3K9me3 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone demethylase activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within cellular response to ionizing radiation	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of protein phosphorylation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in pericentric heterochromatin	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysine-specific demethylase 4D

Names: [histone H3]-trimethyl-L-lysine(9) demethylase 4D; jmjC domain-containing histone demethylation protein 3D; jumonji domain-containing protein 2D; lysine (K)-specific demethylase 4D

NP_001073180.1

EC 1.14.11.66

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001079712.1 → NP_001073180.1 lysine-specific demethylase 4D

See identical proteins and their annotated locations for NP_001073180.1

Status: PROVISIONAL

Source sequence(s)

BC128760

UniProtKB/Swiss-Prot

A1A5Q5

UniProtKB/TrEMBL

A6JN92

Related

ENSRNOP00000099256.1, ENSRNOT00000127250.1

Conserved Domains (2) summary

smart00545
Location:15 → 55

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase