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

Gene ID: 10765, updated on 13-May-2022

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
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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
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202724495..202808421, complement)
110 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 Sharpr-MPRA regulatory region 13308 Neighboring gene synaptotagmin 2 Neighboring gene cytochrome c oxidase subunit 7C pseudogene Neighboring gene solute carrier family 25 member 39 pseudogene 1 Neighboring gene uncharacterized LOC124904583 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. Identification of the upstream regulators of KDM5B in gastric cancer. Zhao LF, et al. Life Sci, 2022 Jun 1. PMID 35248525
  2. Agenesis of the Corpus Callosum with Facial Dysmorphism and Intellectual Disability in Sibs Associated with Compound Heterozygous KDM5B Variants. Lebon S, et al. Genes (Basel), 2021 Sep 10. PMID 34573379, Free PMC Article
  3. KDM5B promotes cell migration by regulating the noncanonical Wnt/PCP pathway in Hirschsprung's disease. Yao T, et al. Pediatr Surg Int, 2022 Jan. PMID 34455465
  4. Histone lysine demethylase KDM5B maintains chronic myeloid leukemia via multiple epigenetic actions. Xue S, et al. Exp Hematol, 2020 Feb. PMID 32007477
  5. Jarid1b promotes epidermal differentiation by mediating the repression of Ship1 and activation of the AKT/Ovol1 pathway. Sun X, et al. Cell Prolif, 2019 Sep. PMID 31152465, Free PMC Article

See all (137) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of the upstream regulators of KDM5B in gastric cancer.
    Title: Identification of the upstream regulators of KDM5B in gastric cancer.
  2. Agenesis of the Corpus Callosum with Facial Dysmorphism and Intellectual Disability in Sibs Associated with Compound Heterozygous KDM5B Variants.
    Title: Agenesis of the Corpus Callosum with Facial Dysmorphism and Intellectual Disability in Sibs Associated with Compound Heterozygous <i>KDM5B</i> Variants.
  3. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.
    Title: KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.
  4. KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance.
    Title: KDM5A and KDM5B histone-demethylases contribute to HU-induced replication stress response and tolerance.
  5. KDM5B promotes cell migration by regulating the noncanonical Wnt/PCP pathway in Hirschsprung's disease.
    Title: KDM5B promotes cell migration by regulating the noncanonical Wnt/PCP pathway in Hirschsprung's disease.
  6. microRNA-486-5p functions as a tumor suppressor in gastric carcinoma via directly targeting KDM5B.
    Title: microRNA-486-5p functions as a tumor suppressor in gastric carcinoma via directly targeting KDM5B.
  7. JARID1B promotes colorectal cancer proliferation and Wnt/beta-catenin signaling via decreasing CDX2 level.
    Title: JARID1B promotes colorectal cancer proliferation and Wnt/β-catenin signaling via decreasing CDX2 level.
  8. Expression and prognostic values of ARID family members in breast cancer.
    Title: Expression and prognostic values of ARID family members in breast cancer.
  9. KDM5B Is Essential for the Hyperactivation of PI3K/AKT Signaling in Prostate Tumorigenesis.
    Title: KDM5B Is Essential for the Hyperactivation of PI3K/AKT Signaling in Prostate Tumorigenesis.
  10. Lysine demethylase 5B suppresses CC chemokine ligand 14 to promote progression of colorectal cancer through the Wnt/beta-catenin pathway.
    Title: Lysine demethylase 5B suppresses CC chemokine ligand 14 to promote progression of colorectal cancer through the Wnt/β-catenin pathway.
Submit: New GeneRIF Correction See all GeneRIFs (93)

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 H3-methyl-lysine-4 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3-methyl-lysine-4 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3-tri/di/monomethyl-lysine-4 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables histone H3-tri/di/monomethyl-lysine-4 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3-tri/di/monomethyl-lysine-4 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 IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables histone demethylase activity TAS
Traceable Author Statement
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 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
 PubMed 
involved_in histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in histone H3-K4 demethylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in histone H3-K4 demethylation, trimethyl-H3-K4-specific IEA
Inferred from Electronic Annotation
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 transcription, DNA-templated 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 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
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
 PubMed 
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

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
    4938..89223
    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/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

  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
    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
    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
    Q9UGL1
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    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

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

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