KDM4B lysine demethylase 4B [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM4Bprovided by HGNC
Official Full Name: lysine demethylase 4Bprovided by HGNC
Primary source: HGNC:HGNC:29136
See related: Ensembl:ENSG00000127663 MIM:609765; AllianceGenome:HGNC:29136
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MRD65; JMJD2B; TDRD14B
Summary: Enables histone H3-methyl-lysine-36 demethylase activity and histone H3-methyl-lysine-9 demethylase activity. Involved in histone H3-K36 demethylation and histone H3-K9 demethylation. Located in cytosol and nucleoplasm. Implicated in autosomal dominant non-syndromic intellectual disability; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Biomarker of several diseases, including alopecia areata; lung cancer; medulloblastoma; prostate cancer; and stomach cancer. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in prostate (RPKM 5.2), thyroid (RPKM 5.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (4969113..5153598)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (4954509..5140176)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (4969124..5153609)

Chromosome 19 - NC_000019.10 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?

KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner.
Title: KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner.
Histone demethylase KDM4B accelerates the progression of glioblastoma via the epigenetic regulation of MYC stability.
Title: Histone demethylase KDM4B accelerates the progression of glioblastoma via the epigenetic regulation of MYC stability.
HIF1alpha-mediated transactivation of WTAP promotes AML cell proliferation via m[6]A-dependent stabilization of KDM4B mRNA.
Title: HIF1α-mediated transactivation of WTAP promotes AML cell proliferation via m(6)A-dependent stabilization of KDM4B mRNA.
Histone demethylase KDM4B contributes to advanced clear cell renal carcinoma and association with copy number variations and cell cycle progression.
Title: Histone demethylase KDM4B contributes to advanced clear cell renal carcinoma and association with copy number variations and cell cycle progression.
Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2.
Title: Histone H3K9 demethylase JMJD2B/KDM4B promotes osteogenic differentiation of bone marrow-derived mesenchymal stem cells by regulating H3K9me2 on RUNX2.
KDM4B, a potential prognostic biomarker revealed by large-scale public databases and clinical samples in uterine corpus endometrial carcinoma.
Title: KDM4B, a potential prognostic biomarker revealed by large-scale public databases and clinical samples in uterine corpus endometrial carcinoma.
Loss of KDM4B impairs osteogenic differentiation of OMSCs and promotes oral bone aging.
Title: Loss of KDM4B impairs osteogenic differentiation of OMSCs and promotes oral bone aging.
KDM4B Overexpression Promotes the Growth, Migration, and Invasion of Rheumatoid Arthritis Fibroblast-Like Synoviocytes by Activating STAT3 Pathway.
Title: KDM4B Overexpression Promotes the Growth, Migration, and Invasion of Rheumatoid Arthritis Fibroblast-Like Synoviocytes by Activating STAT3 Pathway.
IL-13 Augments Histone Demethylase JMJD2B/KDM4B Expression Levels, Activity, and Nuclear Translocation in Airway Fibroblasts in Asthma.
Title: IL-13 Augments Histone Demethylase JMJD2B/KDM4B Expression Levels, Activity, and Nuclear Translocation in Airway Fibroblasts in Asthma.
Targeting KDM4B that coactivates c-Myc-regulated metabolism to suppress tumor growth in castration-resistant prostate cancer.
Title: Targeting KDM4B that coactivates c-Myc-regulated metabolism to suppress tumor growth in castration-resistant prostate cancer.

Submit: New GeneRIF Correction See all GeneRIFs (64)

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

Associated conditions

Description	Tests
Intellectual developmental disorder, autosomal dominant 65 MedGen: C5543371 OMIM: 619320 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D11S2921 (e-PCR)
- UniSTS:152074

RH65659 (e-PCR)
- UniSTS:46920

D16S325 (e-PCR)
- UniSTS:147089

D19S1137 (e-PCR)
- UniSTS:70052

SHGC-149629 (e-PCR)
- UniSTS:183208

WI-15786 (e-PCR)
- UniSTS:28627

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H3K36 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K9 demethylase activity	TAS Traceable Author Statement more info
enables histone H3K9me2/H3K9me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: lysine-specific demethylase 4B

Names: [histone H3]-trimethyl-L-lysine(9) demethylase 4B; jmjC domain-containing histone demethylation protein 3B; jumonji domain containing 2B; jumonji domain-containing protein 2B; lysine (K)-specific demethylase 4B; tudor domain containing 14B

NP_001357022.1

EC 1.14.11.66

NP_001357023.1

EC 1.14.11.66

NP_001398077.1

EC 1.14.11.66

NP_055830.1

EC 1.14.11.66

XP_005259578.2

EC 1.14.11.66

XP_011526116.1

EC 1.14.11.66

XP_011526119.1

EC 1.14.11.66

XP_011526121.1

EC 1.14.11.66

XP_011526122.1

EC 1.14.11.66

XP_011526123.1

EC 1.14.11.66

XP_011526124.1

EC 1.14.11.66

XP_016881992.1

EC 1.14.11.66

XP_016881993.1

EC 1.14.11.66

XP_016881994.1

EC 1.14.11.66

XP_047294426.1

EC 1.14.11.66

XP_047294428.1

EC 1.14.11.66

XP_054176255.1

EC 1.14.11.66

XP_054176256.1

EC 1.14.11.66

XP_054176257.1

EC 1.14.11.66

XP_054176258.1

EC 1.14.11.66

XP_054176259.1

EC 1.14.11.66

XP_054176260.1

EC 1.14.11.66

XP_054176261.1

EC 1.14.11.66

XP_054176262.1

EC 1.14.11.66

XP_054176263.1

EC 1.14.11.66

XP_054176264.1

EC 1.14.11.66

XP_054176265.1

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_001370093.1 → NP_001357022.1 lysine-specific demethylase 4B isoform 2

Status: VALIDATED

Source sequence(s)

AC005595, AC022517, AC053467, AC093033, AC104520

Consensus CDS

CCDS92493.1

Related

ENSP00000371178.3, ENST00000381759.8

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
NM_001370094.1 → NP_001357023.1 lysine-specific demethylase 4B isoform 3

Status: VALIDATED

Source sequence(s)

AC005595, AC022517, AC053467, AC093033, AC104520

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
NM_001411148.1 → NP_001398077.1 lysine-specific demethylase 4B isoform 4

Status: VALIDATED

Source sequence(s)

AC005595, AC022517, AC053467, AC093033, AC104520, KC877698, KC877705

Consensus CDS

CCDS92494.1

UniProtKB/TrEMBL

F5GX28
NM_015015.3 → NP_055830.1 lysine-specific demethylase 4B isoform 1

See identical proteins and their annotated locations for NP_055830.1

Status: VALIDATED

Source sequence(s)

AB020683, AF052144, BC015378, BF917212, DA379611, DB636535

Consensus CDS

CCDS12138.1

UniProtKB/Swiss-Prot

B9EGN8, D6W631, O75274, O94953, Q6P3R5, Q9P1V1, Q9UF40

UniProtKB/TrEMBL

A0A0C4DFL8

Related

ENSP00000159111.3, ENST00000159111.9

Conserved Domains (5) summary

smart00545
Location:15 → 56

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

smart00333
Location:921 → 973

TUDOR; Tudor domain

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase

cd15576
Location:683 → 788

PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

cd15714
Location:797 → 906

ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

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_000019.10 Reference GRCh38.p14 Primary Assembly

Range

4969113..5153598

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005259521.5 → XP_005259578.2 lysine-specific demethylase 4B isoform X1

UniProtKB/TrEMBL

B7ZM63, F5GX28

Related

ENSP00000480642.1, ENST00000611640.4

Conserved Domains (5) summary

smart00545
Location:15 → 56

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

smart00333
Location:955 → 1007

TUDOR; Tudor domain

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase

cd15576
Location:717 → 822

PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

cd15714
Location:831 → 940

ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
XM_011527814.3 → XP_011526116.1 lysine-specific demethylase 4B isoform X3

UniProtKB/TrEMBL

B7ZM63

Conserved Domains (4) summary

smart00333
Location:863 → 915

TUDOR; Tudor domain

pfam02373
Location:84 → 200

JmjC; JmjC domain, hydroxylase

cd15576
Location:625 → 730

PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

cd15714
Location:739 → 848

ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
XM_017026504.3 → XP_016881993.1 lysine-specific demethylase 4B isoform X5
XM_017026505.3 → XP_016881994.1 lysine-specific demethylase 4B isoform X6

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
XM_011527819.3 → XP_011526121.1 lysine-specific demethylase 4B isoform X6

See identical proteins and their annotated locations for XP_011526121.1

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
XM_011527820.3 → XP_011526122.1 lysine-specific demethylase 4B isoform X6

See identical proteins and their annotated locations for XP_011526122.1

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
XM_011527821.3 → XP_011526123.1 lysine-specific demethylase 4B isoform X6

See identical proteins and their annotated locations for XP_011526123.1

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
XM_011527822.3 → XP_011526124.1 lysine-specific demethylase 4B isoform X7

Conserved Domains (2) summary

smart00545
Location:15 → 56

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

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase
XM_047438470.1 → XP_047294426.1 lysine-specific demethylase 4B isoform X1

UniProtKB/TrEMBL

F5GX28
XM_017026503.2 → XP_016881992.1 lysine-specific demethylase 4B isoform X1

UniProtKB/TrEMBL

B7ZM63, F5GX28

Conserved Domains (5) summary

smart00545
Location:15 → 56

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

smart00333
Location:955 → 1007

TUDOR; Tudor domain

pfam02373
Location:176 → 292

JmjC; JmjC domain, hydroxylase

cd15576
Location:717 → 822

PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

cd15714
Location:831 → 940

ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
XM_047438472.1 → XP_047294428.1 lysine-specific demethylase 4B isoform X2

UniProtKB/TrEMBL

A0A0C4DFL8
XM_011527817.3 → XP_011526119.1 lysine-specific demethylase 4B isoform X4

UniProtKB/TrEMBL

B3KX69

Conserved Domains (3) summary

smart00333
Location:595 → 647

TUDOR; Tudor domain

cd15576
Location:357 → 462

PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

cd15714
Location:471 → 580

ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

RNA

XR_007066691.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

4954509..5140176

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054320280.1 → XP_054176255.1 lysine-specific demethylase 4B isoform X1

UniProtKB/TrEMBL

F5GX28
XM_054320286.1 → XP_054176261.1 lysine-specific demethylase 4B isoform X5
XM_054320284.1 → XP_054176259.1 lysine-specific demethylase 4B isoform X8
XM_054320287.1 → XP_054176262.1 lysine-specific demethylase 4B isoform X10
XM_054320288.1 → XP_054176263.1 lysine-specific demethylase 4B isoform X6
XM_054320289.1 → XP_054176264.1 lysine-specific demethylase 4B isoform X6
XM_054320290.1 → XP_054176265.1 lysine-specific demethylase 4B isoform X7
XM_054320281.1 → XP_054176256.1 lysine-specific demethylase 4B isoform X1

UniProtKB/TrEMBL

F5GX28
XM_054320282.1 → XP_054176257.1 lysine-specific demethylase 4B isoform X1

UniProtKB/TrEMBL

F5GX28
XM_054320283.1 → XP_054176258.1 lysine-specific demethylase 4B isoform X2

UniProtKB/TrEMBL

A0A0C4DFL8
XM_054320285.1 → XP_054176260.1 lysine-specific demethylase 4B isoform X9