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

    Gene ID: 10765, updated on 29-Oct-2024

    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_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_000001.11Genomic 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 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. Coordinated regulation of retinoic acid signaling pathway by KDM5B and polycomb repressive complex 2. Zhang Y, et al. J Cell Biochem, 2014 Sep. PMID 24619877
    2. JARID1B expression in human melanoma and benign melanocytic skin lesions. Kuźbicki L, et al. Melanoma Res, 2013 Feb. PMID 23262439
    3. 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
    4. 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
    5. JARID1B Expression Plays a Critical Role in Chemoresistance and Stem Cell-Like Phenotype of Neuroblastoma Cells. Kuo YT, et al. PLoS One, 2015. PMID 25951238, Free PMC Article

    See all (159) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance.
      Title: Lysine demethylase 5B (KDM5B): A key regulator of cancer drug resistance.
    10. 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)

    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
    located_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 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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    NEW Try the new Transcript table

    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
      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_2024_08

    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

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

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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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