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

Gene ID: 10765, updated on 23-Nov-2023

Summary

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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

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See KDM5B in Genome Data Viewer
Location:
1q32.1
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202724495..202808421, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201986695..202071080, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202693623..202777549, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 12B Neighboring gene small nucleolar RNA SNORA70 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202536800-202537472 Neighboring gene Sharpr-MPRA regulatory region 13308 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:202557917-202559116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202560242-202561068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202591842-202592466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202606743-202607308 Neighboring gene synaptotagmin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202611908-202612840 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202626482-202626641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202627175-202627676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202640443-202640943 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202645972-202646140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202671295-202671794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202764986-202765486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202765487-202765987 Neighboring gene COX7C pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1706 Neighboring gene solute carrier family 25 member 39 pseudogene 1 Neighboring gene uncharacterized LOC124904583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1707 Neighboring gene MGAT4 family member E, pseudogene Neighboring gene prostate cancer associated transcript 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. PLU1 Promotes the Proliferation and Migration of Glioma Cells and Regulates Metabolism. Dong W, et al. Technol Cancer Res Treat, 2023 Jan-Dec. PMID 37254514, Free PMC Article
  2. A truncated and catalytically inactive isoform of KDM5B histone demethylase accumulates in breast cancer cells and regulates H3K4 tri-methylation and gene expression. Di Nisio E, et al. Cancer Gene Ther, 2023 Jun. PMID 36697763, Free PMC Article
  3. Pathogenic KDM5B variants in the context of developmental disorders. Harrington J, et al. Biochim Biophys Acta Gene Regul Mech, 2022 Jul. PMID 35905858
  4. H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity. He R, et al. Oncogene, 2022 May. PMID 35440714, Free PMC Article
  5. KDM5B promotes tumorigenesis of Ewing sarcoma via FBXW7/CCNE1 axis. Chen B, et al. Cell Death Dis, 2022 Apr 15. PMID 35428764, Free PMC Article

See all (147) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene.
    Title: Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene.
  2. A truncated and catalytically inactive isoform of KDM5B histone demethylase accumulates in breast cancer cells and regulates H3K4 tri-methylation and gene expression.
    Title: A truncated and catalytically inactive isoform of KDM5B histone demethylase accumulates in breast cancer cells and regulates H3K4 tri-methylation and gene expression.
  3. PLU1 Promotes the Proliferation and Migration of Glioma Cells and Regulates Metabolism.
    Title: PLU1 Promotes the Proliferation and Migration of Glioma Cells and Regulates Metabolism.
  4. Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis.
    Title: Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis.
  5. Pathogenic KDM5B variants in the context of developmental disorders.
    Title: Pathogenic KDM5B variants in the context of developmental disorders.
  6. CUX2/KDM5B/SOX17 Axis Affects the Occurrence and Development of Breast Cancer.
    Title: CUX2/KDM5B/SOX17 Axis Affects the Occurrence and Development of Breast Cancer.
  7. KDM5B promotes tumorigenesis of Ewing sarcoma via FBXW7/CCNE1 axis.
    Title: KDM5B promotes tumorigenesis of Ewing sarcoma via FBXW7/CCNE1 axis.
  8. H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.
    Title: H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.
  9. Overcoming radio-resistance in esophageal squamous cell carcinoma via hypermethylation of PIK3C3 promoter region mediated by KDM5B loss.
    Title: Overcoming radio-resistance in esophageal squamous cell carcinoma via hypermethylation of PIK3C3 promoter region mediated by KDM5B loss.
  10. Identification of the upstream regulators of KDM5B in gastric cancer.
    Title: Identification of the upstream regulators of KDM5B in gastric cancer.
Submit: New GeneRIF Correction See all GeneRIFs (101)

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
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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)

Genotypes

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 PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 histone H3K4 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 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 nucleic acid binding EXP
Inferred from Experiment
more info
 PubMed 
enables nucleic acid binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in 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
  
involved_in cellular response to leukemia inhibitory factor 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
  
involved_in mammary duct terminal end bud growth IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of mammary gland epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in 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
  
involved_in 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
  
involved_in single fertilization IEA
Inferred from Electronic Annotation
more info
  
involved_in uterus morphogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of 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 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 

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
NP_001334520.1
NP_001386746.1
NP_006609.3
XP_011507392.1
XP_011507393.1
XP_054189910.1
XP_054189911.1

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

  1. NG_050659.1 RefSeqGene

    Range
    5987..89913
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    202724495..202808421 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    201986695..202071080 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    Q9UFD3

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

    UniProtKB/TrEMBL
    Q9UFD3
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UGL1.3 GenPept UniProtKB/Swiss-Prot:Q9UGL1

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