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

Gene ID: 23030, updated on 22-Aug-2020

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
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
JMJD2B; TDRD14B
Expression
Ubiquitous expression in prostate (RPKM 5.2), thyroid (RPKM 5.0) and 25 other tissues See more
Orthologs

Genomic context

See KDM4B in Genome Data Viewer
Location:
19p13.3
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (4969087..5153603)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4969123..5153609)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr19.1096 Neighboring gene arrestin domain containing 5 Neighboring gene ubiquitin like with PHD and ring finger domains 1 Neighboring gene microRNA 4747 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene uncharacterized LOC105372253 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
Genome-wide association study of chronic periodontitis in a general German population.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ44906, KIAA0876

Gene Ontology Provided by GOA

Function Evidence Code Pubs
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K36 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone demethylase activity (H3-K9 specific) TAS
Traceable Author Statement
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K36 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
histone methyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
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_055830.1
XP_005259578.2
XP_011526116.1
XP_011526118.1
XP_011526119.1
XP_011526121.1
XP_011526122.1
XP_011526123.1
XP_011526124.1
XP_016881992.1
XP_016881993.1
XP_016881994.1

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.

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
    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_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
    O94953
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    4969087..5153603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    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_017026504.2XP_016881993.1  lysine-specific demethylase 4B isoform X5

  3. XM_017026505.2XP_016881994.1  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
  4. XM_011527819.2XP_011526121.1  lysine-specific demethylase 4B isoform X7

    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
  5. XM_011527820.2XP_011526122.1  lysine-specific demethylase 4B isoform X7

    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
  6. XM_011527821.2XP_011526123.1  lysine-specific demethylase 4B isoform X7

    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
  7. XM_011527822.2XP_011526124.1  lysine-specific demethylase 4B isoform X8

    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_011527814.2XP_011526116.1  lysine-specific demethylase 4B isoform X2

    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)
  9. XM_017026503.1XP_016881992.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    F5GX28
    Related
    ENSP00000440495.1, ENST00000536461.5
    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)
  10. XM_011527817.2XP_011526119.1  lysine-specific demethylase 4B isoform X4

    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)
  11. XM_011527816.2XP_011526118.1  lysine-specific demethylase 4B isoform X3

    Conserved Domains (3) summary
    smart00333
    Location:612664
    TUDOR; Tudor domain
    cd15576
    Location:374479
    PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cd15714
    Location:488597
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)

RNA

  1. XR_936167.2 RNA Sequence

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