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

    Gene ID: 10765, updated on 5-Nov-2017
    Official Symbol
    KDM5Bprovided by HGNC
    Official Full Name
    lysine demethylase 5Bprovided by HGNC
    Primary source
    HGNC:HGNC:18039
    See related
    Ensembl:ENSG00000117139 MIM:605393; Vega:OTTHUMG00000041401
    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; 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
    Location:
    1q32.1
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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_000001.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 12B Neighboring gene ribosomal protein S27 pseudogene 8 Neighboring gene uncharacterized LOC105371686 Neighboring gene synaptotagmin 2 Neighboring gene cytochrome c oxidase subunit 7C pseudogene Neighboring gene solute carrier family 25 member 39 pseudogene 1 Neighboring gene MGAT4 family member E, pseudogene Neighboring gene prostate cancer associated transcript 6 (non-protein coding)

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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

    • 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...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    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 
    dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    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 from RNA polymerase II promoter 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
     
    transcription, DNA-templated 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 
    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

    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_001314042.1NP_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, OTTHUMP00000038816, ENST00000367264.6, OTTHUMT00000099186
      Conserved Domains (8) summary
      smart00501
      Location:98188
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:3172
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:522638
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:347392
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:12141257
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:15221571
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:728780
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7931122
      PLU-1; PLU-1-like protein
    2. NM_001347591.1NP_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
    3. NM_006618.4NP_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, OTTHUMP00000038815, ENST00000367265.7, OTTHUMT00000099184
      Conserved Domains (8) summary
      smart00501
      Location:98188
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:3172
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:486602
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:311356
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:11781221
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:14861535
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:692744
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7571086
      PLU-1; PLU-1-like protein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p7 Primary Assembly

      Range
      202725185..202809470 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509088.2XP_011507390.1  lysine-specific demethylase 5B isoform X1

      Conserved Domains (8) summary
      smart00501
      Location:98188
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:3172
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:441557
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:266311
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:11331176
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:14411490
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:647699
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7121041
      PLU-1; PLU-1-like protein
    2. XM_011509091.2XP_011507393.1  lysine-specific demethylase 5B isoform X2

      See identical proteins and their annotated locations for XP_011507393.1

      Conserved Domains (6) summary
      pfam02373
      Location:364480
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:189234
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:10561099
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:13641413
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:570622
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:635964
      PLU-1; PLU-1-like protein
    3. XM_011509090.2XP_011507392.1  lysine-specific demethylase 5B isoform X2

      See identical proteins and their annotated locations for XP_011507392.1

      Conserved Domains (6) summary
      pfam02373
      Location:364480
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:189234
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:10561099
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:13641413
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:570622
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:635964
      PLU-1; PLU-1-like protein
    4. XM_011509092.2XP_011507394.1  lysine-specific demethylase 5B isoform X3

      Related
      ENSP00000235790.4, OTTHUMP00000197658, ENST00000235790.8, OTTHUMT00000099185
      Conserved Domains (6) summary
      pfam02373
      Location:328444
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:153198
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:10201063
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:13281377
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:534586
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:599928
      PLU-1; PLU-1-like protein

    Alternate CHM1_1.1

    Genomic

    1. NC_018912.2 Alternate CHM1_1.1

      Range
      204116533..204200837 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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