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KDM4B lysine demethylase 4B [ Homo sapiens (human) ]

Gene ID: 23030, updated on 7-Sep-2023

Summary

Official Symbol
KDM4Bprovided by HGNC
Official Full Name
lysine demethylase 4Bprovided by HGNC
Primary source
HGNC:HGNC:29136
See related
Ensembl:ENSG00000127663 MIM:609765; AllianceGenome:HGNC:29136
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRD65; JMJD2B; TDRD14B
Summary
Enables histone H3-methyl-lysine-36 demethylase activity and histone H3-methyl-lysine-9 demethylase activity. Involved in histone H3-K36 demethylation and histone H3-K9 demethylation. Located in cytosol and nucleoplasm. Implicated in autosomal dominant non-syndromic intellectual disability; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Biomarker of several diseases, including alopecia areata; lung cancer; medulloblastoma; prostate cancer; and stomach cancer. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in prostate (RPKM 5.2), thyroid (RPKM 5.0) and 25 other tissues See more
Orthologs
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Genomic context

See KDM4B in Genome Data Viewer
Location:
19p13.3
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (4969113..5153598)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (4954509..5140176)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4969124..5153609)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4890817-4891318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4891319-4891818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4908546-4909452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4923227-4923955 Neighboring gene arrestin domain containing 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4930593-4931092 Neighboring gene ubiquitin like with PHD and ring finger domains 1 Neighboring gene microRNA 4747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4983945-4984871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4988552-4989057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4989058-4989562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4989779-4990280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4990281-4990780 Neighboring gene Sharpr-MPRA regulatory region 13405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5004333-5004833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5026529-5027028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5036688-5037262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5042227-5042746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5042747-5043265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5046625-5047428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5048922-5049524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5052015-5052514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5083429-5084111 Neighboring gene Sharpr-MPRA regulatory region 3293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5092687-5093236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5093237-5093784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5096761-5097261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5095749-5096249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5096260-5096760 Neighboring gene Sharpr-MPRA regulatory region 7356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5109710-5110566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5111029-5111538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5114178-5115133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5115134-5116088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5121454-5121994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5125360-5125896 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5125897-5126434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5126435-5126971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5126972-5127509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5128585-5129120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5129121-5129658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5130196-5130732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5129659-5130195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5130733-5131269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5137253-5137754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5137755-5138254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5151275-5152046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5153977-5154477 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:5172675-5173874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5191478-5192140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5225323-5225942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5225943-5226561 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5268923-5269423 Neighboring gene uncharacterized LOC105372253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5294563-5295180 Neighboring gene ribosomal protein L32 pseudogene 34

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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Intellectual developmental disorder, autosomal dominant 65
MedGen: C5543371 OMIM: 619320 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of chronic periodontitis in a general German population.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ44906, KIAA0876

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone H3K36 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3K9 demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K9 demethylase activity TAS
Traceable Author Statement
more info
 
enables histone H3K9me2/H3K9me3 demethylase activity 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
 
Process Evidence Code Pubs
involved_in brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 4B
Names
[histone H3]-trimethyl-L-lysine(9) demethylase 4B
jmjC domain-containing histone demethylation protein 3B
jumonji domain containing 2B
jumonji domain-containing protein 2B
lysine (K)-specific demethylase 4B
tudor domain containing 14B
NP_001357022.1
NP_001357023.1
NP_001398077.1
NP_055830.1
XP_005259578.2
XP_011526116.1
XP_011526119.1
XP_011526121.1
XP_011526122.1
XP_011526123.1
XP_011526124.1
XP_016881992.1
XP_016881993.1
XP_016881994.1
XP_047294426.1
XP_047294428.1
XP_054176255.1
XP_054176256.1
XP_054176257.1
XP_054176258.1
XP_054176259.1
XP_054176260.1
XP_054176261.1
XP_054176262.1
XP_054176263.1
XP_054176264.1
XP_054176265.1

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001370093.1NP_001357022.1  lysine-specific demethylase 4B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC005595, AC022517, AC053467, AC093033, AC104520
    Consensus CDS
    CCDS92493.1
    Related
    ENSP00000371178.3, ENST00000381759.8
    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  2. NM_001370094.1NP_001357023.1  lysine-specific demethylase 4B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC005595, AC022517, AC053467, AC093033, AC104520
    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  3. NM_001411148.1NP_001398077.1  lysine-specific demethylase 4B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC005595, AC022517, AC053467, AC093033, AC104520, KC877698, KC877705
    Consensus CDS
    CCDS92494.1
    UniProtKB/TrEMBL
    B7ZM63, F5GX28
  4. NM_015015.3NP_055830.1  lysine-specific demethylase 4B isoform 1

    See identical proteins and their annotated locations for NP_055830.1

    Status: VALIDATED

    Source sequence(s)
    AB020683, AF052144, BC015378, BF917212, DA379611, DB636535
    Consensus CDS
    CCDS12138.1
    UniProtKB/Swiss-Prot
    B9EGN8, D6W631, O75274, O94953, Q6P3R5, Q9P1V1, Q9UF40
    UniProtKB/TrEMBL
    A0A0C4DFL8
    Related
    ENSP00000159111.3, ENST00000159111.9
    Conserved Domains (5) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:921973
    TUDOR; Tudor domain
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    cd15576
    Location:683788
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cd15714
    Location:797906
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    4969113..5153598
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259521.5XP_005259578.2  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B7ZM63, F5GX28
    Related
    ENSP00000480642.1, ENST00000611640.4
    Conserved Domains (5) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:9551007
    TUDOR; Tudor domain
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    cd15576
    Location:717822
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cd15714
    Location:831940
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
  2. XM_011527814.3XP_011526116.1  lysine-specific demethylase 4B isoform X3

    UniProtKB/TrEMBL
    B7ZM63
    Conserved Domains (4) summary
    smart00333
    Location:863915
    TUDOR; Tudor domain
    pfam02373
    Location:84200
    JmjC; JmjC domain, hydroxylase
    cd15576
    Location:625730
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cd15714
    Location:739848
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
  3. XM_017026504.3XP_016881993.1  lysine-specific demethylase 4B isoform X5

  4. XM_017026505.3XP_016881994.1  lysine-specific demethylase 4B isoform X6

    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  5. XM_011527819.3XP_011526121.1  lysine-specific demethylase 4B isoform X6

    See identical proteins and their annotated locations for XP_011526121.1

    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  6. XM_011527820.3XP_011526122.1  lysine-specific demethylase 4B isoform X6

    See identical proteins and their annotated locations for XP_011526122.1

    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  7. XM_011527821.3XP_011526123.1  lysine-specific demethylase 4B isoform X6

    See identical proteins and their annotated locations for XP_011526123.1

    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  8. XM_011527822.3XP_011526124.1  lysine-specific demethylase 4B isoform X7

    Conserved Domains (2) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
  9. XM_047438470.1XP_047294426.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B7ZM63, F5GX28
  10. XM_017026503.2XP_016881992.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B7ZM63, F5GX28
    Conserved Domains (5) summary
    smart00545
    Location:1556
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:9551007
    TUDOR; Tudor domain
    pfam02373
    Location:176292
    JmjC; JmjC domain, hydroxylase
    cd15576
    Location:717822
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cd15714
    Location:831940
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
  11. XM_047438472.1XP_047294428.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/Swiss-Prot
    B9EGN8, D6W631, O75274, O94953, Q6P3R5, Q9P1V1, Q9UF40
    UniProtKB/TrEMBL
    A0A0C4DFL8
  12. XM_011527817.3XP_011526119.1  lysine-specific demethylase 4B isoform X4

    UniProtKB/TrEMBL
    B3KX69
    Conserved Domains (3) summary
    smart00333
    Location:595647
    TUDOR; Tudor domain
    cd15576
    Location:357462
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cd15714
    Location:471580
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

RNA

  1. XR_007066691.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    4954509..5140176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320280.1XP_054176255.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B7ZM63, F5GX28
  2. XM_054320286.1XP_054176261.1  lysine-specific demethylase 4B isoform X5

  3. XM_054320284.1XP_054176259.1  lysine-specific demethylase 4B isoform X8

    UniProtKB/TrEMBL
    B7ZM63
  4. XM_054320287.1XP_054176262.1  lysine-specific demethylase 4B isoform X10

  5. XM_054320288.1XP_054176263.1  lysine-specific demethylase 4B isoform X6

  6. XM_054320289.1XP_054176264.1  lysine-specific demethylase 4B isoform X6

  7. XM_054320290.1XP_054176265.1  lysine-specific demethylase 4B isoform X7

  8. XM_054320281.1XP_054176256.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B7ZM63, F5GX28
  9. XM_054320282.1XP_054176257.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B7ZM63, F5GX28
  10. XM_054320283.1XP_054176258.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/Swiss-Prot
    B9EGN8, D6W631, O75274, O94953, Q6P3R5, Q9P1V1, Q9UF40
    UniProtKB/TrEMBL
    A0A0C4DFL8
  11. XM_054320285.1XP_054176260.1  lysine-specific demethylase 4B isoform X9

    UniProtKB/TrEMBL
    B3KX69

RNA

  1. XR_008485126.1 RNA Sequence