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

Gene ID: 10765, updated on 6-Jul-2025
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
NEW
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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

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

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

Products Interactant Other Gene Complex Source Pubs Description

Markers

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 DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K4 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K4 demethylase activity IEA
Inferred from Electronic Annotation
more info
 
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 IEA
Inferred from Electronic Annotation
more info
 
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 metal ion binding IEA
Inferred from Electronic Annotation
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 oxidoreductase activity IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
 
enables zinc ion binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within 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
 
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
involved_in chromatin organization 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
 
acts_upstream_of_or_within mammary duct terminal end bud growth IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of mammary gland epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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
 
acts_upstream_of_or_within 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
 
acts_upstream_of_or_within single fertilization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within uterus morphogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_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 IEA
Inferred from Electronic Annotation
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 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
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

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_001314042.2NP_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: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_001347591.2NP_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_001399817.1NP_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_006618.5NP_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: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: 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_011509091.3XP_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: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_011509090.4XP_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: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

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_054333935.1XP_054189910.1  lysine-specific demethylase 5B isoform X1

    UniProtKB/TrEMBL
    Q9UFD3
  2. XM_054333936.1XP_054189911.1  lysine-specific demethylase 5B isoform X1

    UniProtKB/TrEMBL
    Q9UFD3