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
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

Genomic context

Location:: 1q32.1

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
109	current	GRCh38.p12 (GCF_000001405.38)	1	NC_000001.11 (202725185..202809470, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (202696532..202777549, complement)

Chromosome 1 - NC_000001.11 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: 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 FunctionsWhat's a GeneRIF?

These results enlighten an important role of a miRNA's circuit in regulating JARID1B's activity and suggest new perspectives for epigenetic therapies.
Title: JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer.
High JARID1B expression is associated with Osteosarcoma.
Title: Histone Demethylase JARID1B Is Overexpressed in Osteosarcoma and Upregulates Cyclin D1 Expression via Demethylation of H3K27me3.
In the HCC cell line, Hep3B, KDM5B expression promoted promote tumor cell proliferation and colony formation. Increased expression of KDM5B in HCC tissues, compared with adjacent normal liver tissues, and was associated with larger tumor size, advanced TNM stage, and reduced overall survival in patients with HCC.
Title: Increased Expression of Lysine-Specific Demethylase 5B (KDM5B) Promotes Tumor Cell Growth in Hep3B Cells and is an Independent Prognostic Factor in Patients with Hepatocellular Carcinoma.
Data reinforces the recent observation that the KDM5B haploinsufficiency is not a mechanism involved in intellectual disability and that KDM5B disorder associated with loss of heterozygosity variants is a recessive disorder.
Title: Novel KDM5B splice variants identified in patients with developmental disorders: Functional consequences.
Altered splicing of JARID1B may be important factor increasing melanoma aggressiveness.
Title: Prognostic significance of RBP2-H1 variant of JARID1B in melanoma.
both KDM5A and KDM5B are involved in the lengthening of DICER1
Title: KDM5 lysine demethylases are involved in maintenance of 3'UTR length.
HBx activates the histone demethylase KDM5B and induces hepatic progenitor cell-like features in hepatocellular carcinoma
Title: Hepatitis B virus X protein induces hepatic stem cell-like features in hepatocellular carcinoma by activating KDM5B.
JARID1B directly bound to PI3K/AKT signaling inhibitor SHIP1 gene promoter and decreased SHIP1 gene expression.
Title: Overexpression of JARID1B promotes differentiation via SHIP1/AKT signaling in human hypopharyngeal squamous cell carcinoma.
We established the function of JARID1B in mediating the cancer stem cell potential of G0-like cells and our results expand understanding of its context-specific roles in malignant and normal stem cell homeostasis
Title: JARID1B Enables Transit between Distinct States of the Stem-like Cell Population in Oral Cancers.
KDM5B is up-regulated in esophageal squamous cell carcinoma cells.MiR-194 targets KDM5B to inhibit esophageal squamous cell carcinoma development and progression.
Title: Original Research: miR-194 inhibits proliferation and invasion and promotes apoptosis by targeting KDM5B in esophageal squamous cell carcinoma cells.

Submit: New GeneRIF Correction See all GeneRIFs (66)

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
MENTAL RETARDATION, AUTOSOMAL RECESSIVE 65 MedGen: CN253823 OMIM: 618109 GeneReviews: Not available	not available

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)

HIV-1 interactions

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Replication interactions

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

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

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Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
Chromatin organization, organism-specific biosystem (from REACTOME)
Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
Gene Expression, organism-specific biosystem (from REACTOME)
Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
HDMs demethylate histones, organism-specific biosystem (from REACTOME)
HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
TFAP2 (AP-2) family regulates transcription of cell cycle factors, organism-specific biosystem (from REACTOME)
TFAP2 (AP-2) family regulates transcription of cell cycle factors, organism-specific biosystemTFAP2A and TFAP2C play opposing roles in transcriptional regulation of the CDKN1A (p21) gene locus. While TFAP2A stimulates transcription of the CDKN1A cyclin-dependent kinase inhibitor (Zeng et al. ...
Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors, organism-specific biosystem (from REACTOME)
Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors, organism-specific biosystemThe AP-2 (TFAP2) family of transcription factors includes five proteins in mammals: TFAP2A (AP-2 alpha), TFAP2B (AP-2 beta), TFAP2C (AP-2 gamma), TFAP2D (AP-2 delta) and TFAP2E (AP-2 epsilon). The AP...

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

Homology

Homologs of the KDM5B gene: The KDM5B gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, C.elegans, and frog.
Orthologs from Annotation Pipeline: 228 organisms have orthologs with human gene KDM5B
Orthologs

Clone Names

FLJ10538, FLJ12459, FLJ12491, FLJ16281, FLJ23670

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA binding	IDA Inferred from Direct Assay more info	PubMed
DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
dioxygenase activity	IEA Inferred from Electronic Annotation more info
histone binding	IDA Inferred from Direct Assay more info	PubMed
histone demethylase activity (H3-K4 specific)	IDA Inferred from Direct Assay more info	PubMed
histone demethylase activity (H3-K4 specific)	IMP Inferred from Mutant Phenotype more info	PubMed
histone demethylase activity (H3-dimethyl-K4 specific)	IDA Inferred from Direct Assay more info	PubMed
histone demethylase activity (H3-trimethyl-K4 specific)	IDA Inferred from Direct Assay more info	PubMed
histone demethylase activity (H3-trimethyl-K4 specific)	IMP Inferred from Mutant Phenotype more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
sequence-specific double-stranded DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
zinc ion binding	IDA Inferred from Direct Assay more info	PubMed
zinc ion binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
branching involved in mammary gland duct morphogenesis	IEA Inferred from Electronic Annotation more info
cellular response to fibroblast growth factor stimulus	IEA Inferred from Electronic Annotation more info
cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
histone H3-K4 demethylation	IDA Inferred from Direct Assay more info	PubMed
histone H3-K4 demethylation	IMP Inferred from Mutant Phenotype more info	PubMed
histone H3-K4 demethylation, trimethyl-H3-K4-specific	IEA Inferred from Electronic Annotation more info
lens fiber cell differentiation	IEA Inferred from Electronic Annotation more info
mammary duct terminal end bud growth	IEA Inferred from Electronic Annotation more info
negative regulation of transcription, DNA-templated	IEA Inferred from Electronic Annotation more info
oxidation-reduction process	IEA Inferred from Electronic Annotation more info
positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
positive regulation of mammary gland epithelial cell proliferation	IEA Inferred from Electronic Annotation more info
post-embryonic development	IEA Inferred from Electronic Annotation more info
regulation of estradiol secretion	IEA Inferred from Electronic Annotation more info
regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info
response to fungicide	IEA Inferred from Electronic Annotation more info
rhythmic process	IEA Inferred from Electronic Annotation more info
single fertilization	IEA Inferred from Electronic Annotation more info
uterus morphogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytosol	IDA Inferred from Direct Assay more info
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: lysine-specific demethylase 5B

Names: 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

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

4938..89223

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001314042.1 → 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, AF087481, AI262935

Consensus CDS

CCDS81417.1

UniProtKB/Swiss-Prot

Q9UGL1

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_001347591.1 → 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

Related

ENSP00000497671.1, ENST00000650569.1
NM_006618.4 → 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, AI262935, AJ132440, DA436869

Consensus CDS

CCDS30974.1

UniProtKB/Swiss-Prot

Q9UGL1

Related

ENSP00000356234.3, ENST00000367265.8

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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p12 Primary Assembly

Range

202725185..202809470 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011509091.2 → XP_011507393.1 lysine-specific demethylase 5B isoform X1

See identical proteins and their annotated locations for XP_011507393.1

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_011509090.3 → XP_011507392.1 lysine-specific demethylase 5B isoform X1

See identical proteins and their annotated locations for XP_011507392.1

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_011509092.2 → XP_011507394.1 lysine-specific demethylase 5B isoform X2

Related

ENSP00000497113.1, ENST00000648056.1

Conserved Domains (6) summary

pfam02373
Location:328 → 444

JmjC; JmjC domain, hydroxylase

cd15603
Location:153 → 198

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

cd15607
Location:1020 → 1063

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

cd15687
Location:1328 → 1377

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

pfam02928
Location:534 → 586

zf-C5HC2; C5HC2 zinc finger

pfam08429
Location:599 → 928

PLU-1; PLU-1-like protein