Kdm2a lysine (K)-specific demethylase 2A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm2aprovided by MGI
Official Full Name: lysine (K)-specific demethylase 2Aprovided by MGI
Primary source: MGI:MGI:1354736
See related: Ensembl:ENSMUSG00000054611 AllianceGenome:MGI:1354736
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Fbl7; Cxxc8; Fbl11; Jhdm1; Fbxl11; Gm4560; Jhdm1a; lalina; 100043628; 5530401A10Rik
Summary: Enables unmethylated CpG binding activity. Acts upstream of or within several processes, including chordate embryonic development; heart looping; and positive regulation of macromolecule metabolic process. Located in chromatin. Is expressed in embryo; forebrain; and limb. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human KDM2A (lysine demethylase 2A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 17.5), limb E14.5 (RPKM 16.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 19 A; 19 4.01 cM

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (4366172..4448749, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (4316144..4398721, complement)

Chromosome 19 - NC_000085.7 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

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Testis-specific knockout of Kdm2a reveals nonessential roles in male fertility but partially compromises spermatogenesis.
Title: Testis-specific knockout of Kdm2a reveals nonessential roles in male fertility but partially compromises spermatogenesis.
Maternal Kdm2a-mediated PI3K/Akt signaling and E-cadherin stimulate the morula-to-blastocyst transition revealing crucial roles in early embryonic development.
Title: Maternal Kdm2a-mediated PI3K/Akt signaling and E-cadherin stimulate the morula-to-blastocyst transition revealing crucial roles in early embryonic development.
Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
Title: Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
The histone H3K36 demethylase Fbxl11 plays pivotal roles in the development of retinal late-born cell types.
Title: The histone H3K36 demethylase Fbxl11 plays pivotal roles in the development of retinal late-born cell types.
Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes.
Title: Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes.
Ablation of KDM2A Inhibits Preadipocyte Proliferation and Promotes Adipogenic Differentiation.
Title: Ablation of KDM2A Inhibits Preadipocyte Proliferation and Promotes Adipogenic Differentiation.
SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair.
Title: SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair.
MiR-134-5p Regulates Myocardial Apoptosis and Angiogenesis by Directly Targeting KDM2A After Myocardial Infarction.
Title: MiR-134-5p Regulates Myocardial Apoptosis and Angiogenesis by Directly Targeting KDM2A After Myocardial Infarction.
KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CpG islands CGI)-associated gene promoters. KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters.
Title: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity.
Kdm2a expression may be closely related to cell proliferation
Title: Spatial and temporal expression of histone demethylase, Kdm2a, during murine molar development.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (6) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH124989 (e-PCR)
- UniSTS:161811

RH129222 (e-PCR)
- UniSTS:212530

AW536790 (e-PCR)
- UniSTS:181174

UniSTS:224510 (e-PCR)
- UniSTS:224510

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables catalytic activity	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K36 demethylase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K36me/H3K36me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables unmethylated CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables unmethylated CpG binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by competitive promoter binding	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuroepithelial cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein demethylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in transcription initiation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lysine-specific demethylase 2A

Names: F-box and leucine-rich repeat protein 11; F-box protein containing leucine repeats; F-box/LRR-repeat protein 11; [Histone-H3]-lysine-36 demethylase 1A; jmjC domain-containing histone demethylation protein 1A

NP_001001984.2

EC 1.14.11.27

XP_006531785.1

EC 1.14.11.27

XP_006531786.1

EC 1.14.11.27

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_001001984.2 → NP_001001984.2 lysine-specific demethylase 2A

See identical proteins and their annotated locations for NP_001001984.2

Status: VALIDATED

Source sequence(s)

AC140073, AK173084, BC076576, CB246224

Consensus CDS

CCDS37886.1

UniProtKB/Swiss-Prot

P59997, Q3U1M5, Q3UR56, Q3V3Q1, Q69ZT4

UniProtKB/TrEMBL

F6YRW4

Related

ENSMUSP00000076698.5, ENSMUST00000075856.11

Conserved Domains (7) summary

cd09293
Location:931 → 1137

AMN1; Antagonist of mitotic exit network protein 1

sd00034
Location:929 → 953

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:619 → 675

PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)

pfam02008
Location:576 → 609

zf-CXXC; CXXC zinc finger domain

pfam12937
Location:895 → 933

F-box-like

pfam17811
Location:304 → 339

JHD; Jumonji helical domain

cl21464
Location:199 → 299

cupin_like; Conserved domain found in cupin and related proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000085.7 Reference GRCm39 C57BL/6J

Range

4366172..4448749 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006531722.4 → XP_006531785.1 lysine-specific demethylase 2A isoform X1

See identical proteins and their annotated locations for XP_006531785.1

UniProtKB/Swiss-Prot

P59997, Q3U1M5, Q3UR56, Q3V3Q1, Q69ZT4

UniProtKB/TrEMBL

F6YRW4

Related

ENSMUSP00000047683.8, ENSMUST00000047898.14

Conserved Domains (7) summary

cd09293
Location:931 → 1137

AMN1; Antagonist of mitotic exit network protein 1

sd00034
Location:929 → 953

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:619 → 675

PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)

pfam02008
Location:576 → 609

zf-CXXC; CXXC zinc finger domain

pfam12937
Location:895 → 933

F-box-like

pfam17811
Location:304 → 339

JHD; Jumonji helical domain

cl21464
Location:199 → 299

cupin_like; Conserved domain found in cupin and related proteins
XM_006531723.4 → XP_006531786.1 lysine-specific demethylase 2A isoform X2

Conserved Domains (5) summary

cd09293
Location:491 → 697

AMN1; Antagonist of mitotic exit network protein 1

sd00034
Location:489 → 513

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:179 → 235

PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)

pfam02008
Location:136 → 169

zf-CXXC; CXXC zinc finger domain

pfam12937
Location:455 → 493

F-box-like