KDM5B lysine demethylase 5B [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM5Bprovided by HGNC
Official Full Name: lysine demethylase 5Bprovided by HGNC
Primary source: HGNC:HGNC:18039
See related: Ensembl:ENSG00000117139 MIM:605393; AllianceGenome:HGNC:18039
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: CT31; PLU1; PUT1; MRT65; PLU-1; JARID1B; PPP1R98; RBP2-H1; RBBP2H1A
Summary: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
Expression: Broad expression in testis (RPKM 55.0), skin (RPKM 8.8) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q32.1

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (202724495..202808421, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (201986695..202071080, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (202693623..202777549, complement)

Chromosome 1 - NC_000001.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LncRNA HOXC-AS3 accelerates malignant proliferation of cervical cancer cells via stabilizing KDM5B.
Title: LncRNA HOXC-AS3 accelerates malignant proliferation of cervical cancer cells via stabilizing KDM5B.
AUP1 transcriptionally activated by KDM5B reprograms lipid metabolism to promote the malignant progression of cervical cancer.
Title: AUP1 transcriptionally activated by KDM5B reprograms lipid metabolism to promote the malignant progression of cervical cancer.
A Genotype/Phenotype Study of KDM5B-Associated Disorders Suggests a Pathogenic Effect of Dominantly Inherited Missense Variants.
Title: A Genotype/Phenotype Study of KDM5B-Associated Disorders Suggests a Pathogenic Effect of Dominantly Inherited Missense Variants.
ETS homologous factor, controlled by lysine-specific demethylase 5B, suppresses clear cell renal cell carcinoma by inducing Filamin-B.
Title: ETS homologous factor, controlled by lysine-specific demethylase 5B, suppresses clear cell renal cell carcinoma by inducing Filamin-B.
Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
Title: Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization.
KDM5B promotes metastasis and epithelial-mesenchymal transition via Wnt/beta-catenin pathway in squamous cell carcinoma of the head and neck.
Title: KDM5B promotes metastasis and epithelial-mesenchymal transition via Wnt/β-catenin pathway in squamous cell carcinoma of the head and neck.
Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis.
Title: Histone lysine demethylase KDM5B facilitates proliferation and suppresses apoptosis in human acute myeloid leukemia cells through the miR-140-3p/BCL2 axis.
Deubiquitinase USP7 stabilizes KDM5B and promotes tumor progression and cisplatin resistance in nasopharyngeal carcinoma through the ZBTB16/TOP2A axis.
Title: Deubiquitinase USP7 stabilizes KDM5B and promotes tumor progression and cisplatin resistance in nasopharyngeal carcinoma through the ZBTB16/TOP2A axis.
Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance.
Title: Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance.
Long Noncoding RNA HOXA-AS2 Facilitates Prostate Cancer Progression by Inhibiting miR-885-5p to Upregulate KDM5B.
Title: Long Noncoding RNA HOXA-AS2 Facilitates Prostate Cancer Progression by Inhibiting miR-885-5p to Upregulate KDM5B.

Submit: New GeneRIF Correction See all GeneRIFs (110)

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 disability, autosomal recessive 65 MedGen: C4748219 OMIM: 618109 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-01-04) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2018-01-04) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interaction	Pubs
Knockdown of lysine (K)-specific demethylase 5B (KDM5B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69432 (e-PCR)
- UniSTS:87352

SHGC-32074 (e-PCR)
- UniSTS:83040

RH12289 (e-PCR)
- UniSTS:21344

AL009885 (e-PCR)
- UniSTS:66672

RH120083 (e-PCR)
- UniSTS:133513

SHGC-149068 (e-PCR)
- UniSTS:176779

D1S1875E (e-PCR)
- UniSTS:42155

SHGC-76133 (e-PCR)
- UniSTS:63426

JARID1B_3532 (e-PCR)
- UniSTS:462284

Clone Names

FLJ10538, FLJ12459, FLJ12491, FLJ16281, FLJ23670

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables dioxygenase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone binding	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
enables nucleic acid binding	EXP Inferred from Experiment more info	PubMed
enables nucleic acid binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within branching involved in mammary gland duct morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cellular response to fibroblast growth factor stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in lens fiber cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mammary duct terminal end bud growth	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of mammary gland epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of estradiol secretion	IEA Inferred from Electronic Annotation more info
involved_in response to fungicide	IEA Inferred from Electronic Annotation more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within single fertilization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within uterus morphogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: lysine-specific demethylase 5B

Names: [histone H3]-trimethyl-L-lysine(4) demethylase 5B; cancer/testis antigen 31; histone demethylase JARID1B; jumonji, AT rich interactive domain 1B; jumonji/ARID domain-containing protein 1B; lysine (K)-specific demethylase 5B; protein phosphatase 1, regulatory subunit 98; putative DNA/chromatin binding motif; retinoblastoma-binding protein 2 homolog 1; retinoblastoma-binding protein 2, homolog 1A

NP_001300971.1

EC 1.14.11.67

NP_001334520.1

EC 1.14.11.67

NP_001386746.1

EC 1.14.11.67

NP_006609.3

EC 1.14.11.67

XP_011507392.1

EC 1.14.11.67

XP_011507393.1

EC 1.14.11.67

XP_054189910.1

EC 1.14.11.67

XP_054189911.1

EC 1.14.11.67

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.

Genomic

NG_050659.1 RefSeqGene

Range

5987..89913

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001314042.2 → NP_001300971.1 lysine-specific demethylase 5B isoform 1

Status: REVIEWED

Description

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

Source sequence(s)

AC098934, AC104463

Consensus CDS

CCDS81417.1

UniProtKB/TrEMBL

A0A3B3ITJ7

Related

ENSP00000356233.2, ENST00000367264.7

Conserved Domains (8) summary

smart00501
Location:98 → 188

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:31 → 72

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

pfam02373
Location:522 → 638

JmjC; JmjC domain, hydroxylase

cd15603
Location:347 → 392

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1214 → 1257

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1522 → 1571

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02928
Location:728 → 780

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:793 → 1122

PLU-1; PLU-1-like protein
NM_001347591.2 → NP_001334520.1 lysine-specific demethylase 5B isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two exons in the 5' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.

Source sequence(s)

AC098934, AC104463

Consensus CDS

CCDS91143.1

UniProtKB/TrEMBL

A0A3B3ITA8, A0A3B3ITJ7

Related

ENSP00000497671.1, ENST00000650569.1
NM_001399817.1 → NP_001386746.1 lysine-specific demethylase 5B isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site for exon 1 compared to variant 1. The encoded isoform (4) is shorter than isoform 1.

Source sequence(s)

AC098934, AC104463

Consensus CDS

CCDS91144.1

UniProtKB/TrEMBL

A0A3B3IS40, A0A3B3ITJ7

Related

ENSP00000497113.1, ENST00000648056.1
NM_006618.5 → NP_006609.3 lysine-specific demethylase 5B isoform 2

See identical proteins and their annotated locations for NP_006609.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC098934, AC104463

Consensus CDS

CCDS30974.1

UniProtKB/Swiss-Prot

O95811, Q15752, Q9UGL1, Q9Y3Q5

UniProtKB/TrEMBL

A0A3B3ITJ7

Related

ENSP00000356234.3, ENST00000367265.9

Conserved Domains (8) summary

smart00501
Location:98 → 188

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

smart00545
Location:31 → 72

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

pfam02373
Location:486 → 602

JmjC; JmjC domain, hydroxylase

cd15603
Location:311 → 356

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1178 → 1221

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1486 → 1535

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02928
Location:692 → 744

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:757 → 1086

PLU-1; PLU-1-like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

202724495..202808421 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011509091.3 → XP_011507393.1 lysine-specific demethylase 5B isoform X1

See identical proteins and their annotated locations for XP_011507393.1

UniProtKB/TrEMBL

Q9UFD3

Conserved Domains (6) summary

pfam02373
Location:364 → 480

JmjC; JmjC domain, hydroxylase

cd15603
Location:189 → 234

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1056 → 1099

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1364 → 1413

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02928
Location:570 → 622

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:635 → 964

PLU-1; PLU-1-like protein
XM_011509090.4 → XP_011507392.1 lysine-specific demethylase 5B isoform X1

See identical proteins and their annotated locations for XP_011507392.1

UniProtKB/TrEMBL

Q9UFD3

Related

ENSP00000235790.4, ENST00000235790.9

Conserved Domains (6) summary

pfam02373
Location:364 → 480

JmjC; JmjC domain, hydroxylase

cd15603
Location:189 → 234

PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)

cd15607
Location:1056 → 1099

PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)

cd15687
Location:1364 → 1413

PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)

pfam02928
Location:570 → 622

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:635 → 964

PLU-1; PLU-1-like protein

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

201986695..202071080 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054333935.1 → XP_054189910.1 lysine-specific demethylase 5B isoform X1

UniProtKB/TrEMBL

Q9UFD3
XM_054333936.1 → XP_054189911.1 lysine-specific demethylase 5B isoform X1

UniProtKB/TrEMBL

Q9UFD3