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

    Gene ID: 23030, updated on 3-Dec-2024

    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 H3K36 demethylase activity and histone H3K9me2/H3K9me3 demethylase activity. Predicted to be involved in brain development; chromatin remodeling; and regulation of gene expression. Located in cytosol and nucleoplasm. Implicated in autosomal dominant intellectual developmental disorder; 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, Nov 2024]
    Expression
    Ubiquitous expression in prostate (RPKM 5.2), thyroid (RPKM 5.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KDM4B in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (4969113..5153598)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (4954509..5140176)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid silent region 9913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13788 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 ATAC-STARR-seq lymphoblastoid silent region 9914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4983945-4984871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4988552-4989057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4989779-4990280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4989058-4989562 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 ATAC-STARR-seq lymphoblastoid active region 13791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13792 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_chr19:5129659-5130195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5130196-5130732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5130733-5131269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5137253-5137754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5137755-5138254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13797 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5151275-5152046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5153977-5154477 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5165571-5165790 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:5172675-5173874 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5173956-5174147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5191478-5192140 Neighboring gene PTPRS antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5225323-5225942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5225943-5226561 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5247733-5247924 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5268923-5269423 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
     
    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
     
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    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_2024_08

    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