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

Gene ID: 10765, updated on 21-Apr-2019

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

Genomic context

See KDM5B in Genome Data Viewer
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_000001.11Genomic 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

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

HIV-1 interactions

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

  • 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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10538, FLJ12459, FLJ12491, FLJ16281, FLJ23670

Gene Ontology Provided by GOA

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

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)

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, ENST00000367264.7
    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
    Related
    ENSP00000497671.1, ENST00000650569.1
  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, ENST00000367265.8
    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 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011509091.2XP_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: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
  2. XM_011509090.3XP_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: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_011509092.2XP_011507394.1  lysine-specific demethylase 5B isoform X2

    Related
    ENSP00000497113.1, ENST00000648056.1
    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
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