Kdm4a lysine demethylase 4A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Kdm4aprovided by RGD
Official Full Name: lysine demethylase 4Aprovided by RGD
Primary source: RGD:1306378
See related: EnsemblRapid:ENSRNOG00000019956 AllianceGenome:RGD:1306378
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
Also known as: Jmjd2a
Summary: Predicted to enable several functions, including histone H3 demethylase activity; ubiquitin protein ligase binding activity; and zinc ion binding activity. Involved in several processes, including apoptotic chromosome condensation; negative regulation of astrocyte differentiation; and positive regulation of neuron differentiation. Predicted to be located in cytosol; nuclear lumen; and pericentric heterochromatin. Predicted to be active in nucleus. Orthologous to human KDM4A (lysine demethylase 4A). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 218.9), Adrenal (RPKM 186.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (136958178..137004942, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (131672754..131719534, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (136967650..137014402, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Spinal nerve transection-induced upregulation of KDM4A in the dorsal root ganglia contributes to the development and maintenance of neuropathic pain via promoting CCL2 expression in rats.
Title: Spinal nerve transection-induced upregulation of KDM4A in the dorsal root ganglia contributes to the development and maintenance of neuropathic pain via promoting CCL2 expression in rats.
MicroRNA-137-mediated lysine demethylase 4A regulates the recovery of spinal cord injury via the SFRP4-Wnt/beta-Catenin axis.
Title: MicroRNA-137-mediated lysine demethylase 4A regulates the recovery of spinal cord injury via the SFRP4-Wnt/β-Catenin axis.
Histone Demethylase KDM4A Inhibition Represses Neuroinflammation and Improves Functional Recovery in Ischemic Stroke.
Title: Histone Demethylase KDM4A Inhibition Represses Neuroinflammation and Improves Functional Recovery in Ischemic Stroke.
Lysine-Specific Demethylase 4A Regulates Osteogenic Differentiation via Regulating the Binding Ability of H3K9me3 with the Promoters of Runx2, Osterix and Osteocalcin.
Title: Lysine-Specific Demethylase 4A Regulates Osteogenic Differentiation via Regulating the Binding Ability of H3K9me3 with the Promoters of Runx2, Osterix and Osteocalcin.
Data indicate that histone demethylases KDM4A/C regulate H3K9 and H3K36 methylation on brain-derived neurotrophic factor (BDNF) versus astroglial glial fibrillary acidic protein (GFAP) genes in neural stem cells.
Title: Gene-specific methylation control of H3K9 and H3K36 on neurotrophic BDNF versus astroglial GFAP genes by KDM4A/C regulates neural stem cell differentiation.

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General gene information

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Markers

UniSTS:495405 (e-PCR)
- UniSTS:495405

RH79804 (e-PCR)
- UniSTS:92013

BE102827 (e-PCR)
- UniSTS:244372

RH137800 (e-PCR)
- UniSTS:219887

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	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 methylated histone binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in apoptotic chromosome condensation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac muscle hypertrophy in response to stress	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of astrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of autophagy	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to nutrient levels	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in fibrillar center	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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

General protein information

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Preferred Names: lysine-specific demethylase 4A

Names: jumonji domain containing 2A; lysine (K)-specific demethylase 4A

NP_001101436.1

EC 1.14.11.-

XP_006238730.2

EC 1.14.11.-

XP_017448880.1

EC 1.14.11.-

XP_038965929.1

EC 1.14.11.-

XP_063143810.1

EC 1.14.11.-

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_001107966.1 → NP_001101436.1 lysine-specific demethylase 4A

See identical proteins and their annotated locations for NP_001101436.1

Status: PROVISIONAL

Source sequence(s)

CH474008

UniProtKB/TrEMBL

A6JZG4, D4A2N4

Related

ENSRNOP00000061752.1, ENSRNOT00000066165.4

Conserved Domains (4) summary

smart00333
Location:862 → 917

TUDOR; Tudor domain

pfam02373
Location:84 → 200

JmjC; JmjC domain, hydroxylase

cd15575
Location:574 → 673

PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)

cd15713
Location:682 → 791

ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

136958178..137004942 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017593391.3 → XP_017448880.1 lysine-specific demethylase 4A isoform X1

UniProtKB/TrEMBL

A0A0G2K5I7

Related

ENSRNOP00000073442.1, ENSRNOT00000091866.3
XM_006238668.4 → XP_006238730.2 lysine-specific demethylase 4A isoform X1

UniProtKB/TrEMBL

A0A0G2K5I7

Related

ENSRNOP00000109491.1, ENSRNOT00000169258.1
XM_039110001.2 → XP_038965929.1 lysine-specific demethylase 4A isoform X3

Conserved Domains (4) summary

pfam02373
Location:1 → 112

JmjC; JmjC domain, hydroxylase

cd20463
Location:718 → 772

Tudor_JMJD2A_rpt1; first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins

cd20466
Location:775 → 830

Tudor_JMJD2A_rpt2; second Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins

cl22851
Location:594 → 703

PHD_SF; PHD finger superfamily
XM_063287740.1 → XP_063143810.1 lysine-specific demethylase 4A isoform X2

UniProtKB/TrEMBL

A6JZG4, D4A2N4