KDM2A lysine demethylase 2A [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM2Aprovided by HGNC
Official Full Name: lysine demethylase 2Aprovided by HGNC
Primary source: HGNC:HGNC:13606
See related: Ensembl:ENSG00000173120 MIM:605657; AllianceGenome:HGNC:13606
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FBL7; CXXC8; FBL11; FBXL11; JHDM1A; LILINA
Summary: This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Expression: Ubiquitous expression in testis (RPKM 25.2), bone marrow (RPKM 22.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.2

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (67119263..67258082)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (67110939..67252047)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (66886734..67025553)

Chromosome 11 - NC_000011.10 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Biological Functions of the KDM2 Family of Histone Demethylases.
Title: Biological Functions of the KDM2 Family of Histone Demethylases.
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.
Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance.
Title: Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance.
Stabilization of nuclear beta-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance.
Title: Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance.
Histone demethylase KDM2A suppresses EGF-TSPAN8 pathway to inhibit breast cancer cell migration and invasion in vitro.
Title: Histone demethylase KDM2A suppresses EGF-TSPAN8 pathway to inhibit breast cancer cell migration and invasion in vitro.
KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma.
Title: KDM2A plays a dual role in regulating the expression of malignancy-related genes in esophageal squamous cell carcinoma.
NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition.
Title: NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition.
Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3.
Title: Histone H3K36me2 demethylase KDM2A promotes bladder cancer progression through epigenetically silencing RARRES3.
Up-regulation of miR-663a inhibits the cancer stem cell-like properties of glioma via repressing the KDM2A-mediated TGF-beta/SMAD signaling pathway.
Title: Up-regulation of miR-663a inhibits the cancer stem cell-like properties of glioma via repressing the KDM2A-mediated TGF-β/SMAD signaling pathway.
Nuclear receptor binding SET domain protein 1 promotes epithelial-mesenchymal transition in paclitaxel-resistant breast cancer cells via regulating nuclear factor kappa B and F-box and leucine-rich repeat protein 11.
Title: Nuclear receptor binding SET domain protein 1 promotes epithelial-mesenchymal transition in paclitaxel-resistant breast cancer cells via regulating nuclear factor kappa B and F-box and leucine-rich repeat protein 11.

Submit: New GeneRIF Correction See all GeneRIFs (46)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH18199 (e-PCR)
- UniSTS:32010

RH124989 (e-PCR)
- UniSTS:161811

G09895 (e-PCR)
- UniSTS:22603

RH65398 (e-PCR)
- UniSTS:35161

STS-N24829 (e-PCR)
- UniSTS:40567

RH45252 (e-PCR)
- UniSTS:6534

FBXL11 (e-PCR)
- UniSTS:504723

STS-H69553 (e-PCR)
- UniSTS:59039

AFMA190YD5 (e-PCR)
- UniSTS:43181

RH44634 (e-PCR)
- UniSTS:4026

D11S4540 (e-PCR)
- UniSTS:42438

MARC_17215-17216:1023895331:5 (e-PCR)
- UniSTS:268254

RH12099 (e-PCR)
- UniSTS:32485

STS-R06543 (e-PCR)
- UniSTS:58101

STS-Z40471 (e-PCR)
- UniSTS:42495

Clone Names

FLJ00115, FLJ46431, KIAA1004, DKFZp434M1735

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H3K36 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
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 histone demethylase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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 zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by competitive promoter binding	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	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 chromosome	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: lysine-specific demethylase 2A

Names: CXXC-type zinc finger protein 8; F-box and leucine-rich repeat protein 11; F-box/LRR-repeat protein 11; [Histone-H3]-lysine-36 demethylase 1A; jmjC domain-containing histone demethylation protein 1A; jumonji C domain-containing histone demethylase 1A; lysine (K)-specific demethylase 2A

NP_001243334.1

EC 1.14.11.27

NP_036440.1

EC 1.14.11.27

XP_006718543.1

EC 1.14.11.27

XP_011543163.1

EC 1.14.11.27

XP_016872880.1

EC 1.14.11.27

XP_016872881.1

EC 1.14.11.27

XP_047282579.1

EC 1.14.11.27

XP_054224095.1

EC 1.14.11.27

XP_054224096.1

EC 1.14.11.27

XP_054224097.1

EC 1.14.11.27

XP_054224098.1

EC 1.14.11.27

XP_054224099.1

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_001256405.2 → NP_001243334.1 lysine-specific demethylase 2A isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks several 5' exons but contains an alternate 5' exon, uses an internal downstream promoter, and differs in its 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b, also known as SF-KDM2A or short-form KDM2A) has a distinct and shorter N-terminus, compared to isoform a.

Source sequence(s)

AB490246, AI185920, AL117517, AP001885, DR001963

Consensus CDS

CCDS58148.1

UniProtKB/Swiss-Prot

Q9Y2K7

Related

ENSP00000435776.1, ENST00000530342.2

Conserved Domains (5) summary

cd09293
Location:493 → 699

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:137 → 170

zf-CXXC; CXXC zinc finger domain

sd00034
Location:491 → 515

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:180 → 236

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

pfam12937
Location:457 → 497

F-box-like; F-box-like
NM_012308.3 → NP_036440.1 lysine-specific demethylase 2A isoform a

See identical proteins and their annotated locations for NP_036440.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).

Source sequence(s)

AF179221, AP000729, AP001885, BC047486, BC064360, BE675843

Consensus CDS

CCDS44657.1

UniProtKB/Swiss-Prot

D4QA03, E9PIL6, I3VM55, Q49A21, Q4G0M3, Q69YY8, Q9BVH5, Q9H7H5, Q9UK66, Q9Y2K7

UniProtKB/TrEMBL

I3VM53

Related

ENSP00000432786.1, ENST00000529006.7

Conserved Domains (6) summary

pfam02008
Location:576 → 609

zf-CXXC; CXXC zinc finger domain

sd00034
Location:930 → 954

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:619 → 675

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

pfam12937
Location:896 → 934

F-box-like; F-box-like

cl21464
Location:199 → 299

cupin_like; Conserved domain found in cupin and related proteins

cl28166
Location:932 → 1138

AMN1; Antagonist of mitotic exit network protein 1

RNA

NR_027473.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AP000729, AP001885, BC047486, BE675843

Related

ENST00000398645.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

67119263..67258082

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017017391.2 → XP_016872880.1 lysine-specific demethylase 2A isoform X1

UniProtKB/TrEMBL

I3VM54

Related

ENSP00000309302.6, ENST00000308783.9

Conserved Domains (8) summary

cd09293
Location:915 → 1121

AMN1; Antagonist of mitotic exit network protein 1

sd00034
Location:913 → 937

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:602 → 658

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

pfam02008
Location:559 → 592

zf-CXXC; CXXC zinc finger domain

pfam12937
Location:879 → 917

F-box-like

pfam17811
Location:287 → 322

JHD; Jumonji helical domain

cd21784
Location:433 → 500

CTD_KDM2A; C-terminal domain found in Lysine-specific demethylase 2A

cl40423
Location:182 → 282

cupin_RmlC-like; RmlC-like cupin superfamily
XM_017017392.2 → XP_016872881.1 lysine-specific demethylase 2A isoform X1

UniProtKB/TrEMBL

I3VM54

Conserved Domains (8) summary

cd09293
Location:915 → 1121

AMN1; Antagonist of mitotic exit network protein 1

sd00034
Location:913 → 937

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:602 → 658

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

pfam02008
Location:559 → 592

zf-CXXC; CXXC zinc finger domain

pfam12937
Location:879 → 917

F-box-like

pfam17811
Location:287 → 322

JHD; Jumonji helical domain

cd21784
Location:433 → 500

CTD_KDM2A; C-terminal domain found in Lysine-specific demethylase 2A

cl40423
Location:182 → 282

cupin_RmlC-like; RmlC-like cupin superfamily
XM_047426623.1 → XP_047282579.1 lysine-specific demethylase 2A isoform X2
XM_006718480.4 → XP_006718543.1 lysine-specific demethylase 2A isoform X3

Conserved Domains (6) summary

cd09293
Location:837 → 1043

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:481 → 514

zf-CXXC; CXXC zinc finger domain

sd00034
Location:835 → 859

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:524 → 580

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

pfam12937
Location:801 → 841

F-box-like; F-box-like

cl21464
Location:104 → 204

cupin_like; Conserved domain found in cupin and related proteins
XM_011544861.2 → XP_011543163.1 lysine-specific demethylase 2A isoform X4

UniProtKB/Swiss-Prot

Q9Y2K7

Related

ENST00000526258.5

Conserved Domains (5) summary

cd09293
Location:626 → 832

AMN1; Antagonist of mitotic exit network protein 1

pfam02008
Location:270 → 303

zf-CXXC; CXXC zinc finger domain

sd00034
Location:624 → 648

LRR_AMN1; leucine-rich repeat [structural motif]

cd15643
Location:313 → 369

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

pfam12937
Location:590 → 630

F-box-like; F-box-like

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

67110939..67252047

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054368120.1 → XP_054224095.1 lysine-specific demethylase 2A isoform X1

UniProtKB/TrEMBL

I3VM54
XM_054368121.1 → XP_054224096.1 lysine-specific demethylase 2A isoform X1

UniProtKB/TrEMBL

I3VM54
XM_054368122.1 → XP_054224097.1 lysine-specific demethylase 2A isoform X2
XM_054368123.1 → XP_054224098.1 lysine-specific demethylase 2A isoform X3
XM_054368124.1 → XP_054224099.1 lysine-specific demethylase 2A isoform X4