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Kdm4b lysine demethylase 4B [ Rattus norvegicus (Norway rat) ]

Gene ID: 301128, updated on 10-Jul-2024

Summary

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Official Symbol
Kdm4bprovided by RGD
Official Full Name
lysine demethylase 4Bprovided by RGD
Primary source
RGD:1588576
See related
EnsemblRapid:ENSRNOG00000049221 AllianceGenome:RGD:1588576
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable histone H3-methyl-lysine-36 demethylase activity and histone H3-methyl-lysine-9 demethylase activity. Predicted to be involved in chromatin remodeling. Predicted to act upstream of or within histone H3-K36 demethylation; histone H3-K9 demethylation; and negative regulation of histone H3-K9 trimethylation. Located in nucleus. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 97.0), Brain (RPKM 96.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Kdm4b in Genome Data Viewer
Location:
9q11
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (1245885..1324384)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (1158737..1237233)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (10656035..10734127, complement)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene arrestin domain containing 5 Neighboring gene ubiquitin-like with PHD and ring finger domains 1 Neighboring gene ribosomal protein S27 like 3 Neighboring gene transfer RNA lysine (anticodon CUU) 11 Neighboring gene protein tyrosine phosphatase, receptor type, S Neighboring gene zinc and ring finger 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B. Zhang Y, et al. Mol Cell Biochem, 2020 Sep. PMID 32594337
  2. Microarray comparative genomic hybridization detection of copy number changes in desmoplastic melanoma and malignant peripheral nerve sheath tumor. Pryor JG, et al. Am J Dermatopathol, 2011 Dec. PMID 21785329
  3. JMJD2B promotes epithelial-mesenchymal transition by cooperating with β-catenin and enhances gastric cancer metastasis. Zhao L, et al. Clin Cancer Res, 2013 Dec 1. PMID 24077348
  4. Histone demethylase JMJD2B is required for tumor cell proliferation and survival and is overexpressed in gastric cancer. Li W, et al. Biochem Biophys Res Commun, 2011 Dec 16. PMID 22133676
  5. The histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6. Toyokawa G, et al. Cancer Prev Res (Phila), 2011 Dec. PMID 21930796

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B.
    Title: Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables histone H3K36 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K9me2/H3K9me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in brain development ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
lysine-specific demethylase 4B
Names
lysine (K)-specific demethylase 4B
NP_001037701.2
NP_001382562.1
XP_006244381.1
XP_006244382.1
XP_038939071.1
XP_038939072.1
XP_063122897.1
XP_063122898.1
XP_063122899.1

NCBI Reference Sequences (RefSeq)

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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_001044236.3 → NP_001037701.2  lysine-specific demethylase 4B isoform 1

    See identical proteins and their annotated locations for NP_001037701.2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000009
    UniProtKB/TrEMBL
    A0A0G2JXG2, A6KQY4, M0RB75
    Related
    ENSRNOP00000066803.1, ENSRNOT00000071199.4
    Conserved Domains (7) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15714
    Location:798 → 907
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    pfam11725
    Location:475 → 671
    AvrE; Pathogenicity factor
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    cd20464
    Location:920 → 973
    Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
    cl02573
    Location:977 → 1032
    Tudor_SF; Tudor domain superfamily
    cl22851
    Location:686 → 789
    PHD_SF; PHD finger superfamily

  2. NM_001395633.1 → NP_001382562.1  lysine-specific demethylase 4B isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000009
    UniProtKB/TrEMBL
    A0A0G2JXG2
    Conserved Domains (7) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    PHA03247
    Location:327 → 739
    PHA03247; large tegument protein UL36; Provisional
    cd15714
    Location:792 → 901
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    cd20464
    Location:914 → 967
    Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
    cl02573
    Location:971 → 1026
    Tudor_SF; Tudor domain superfamily
    cl22851
    Location:680 → 783
    PHD_SF; PHD finger superfamily

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086027.1 Reference GRCr8

    Range
    1245885..1324384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063266828.1 → XP_063122898.1  lysine-specific demethylase 4B isoform X6

  2. XM_063266829.1 → XP_063122899.1  lysine-specific demethylase 4B isoform X7

  3. XM_039083143.2 → XP_038939071.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    A0A0G2JXG2, A6KQY4, M0RB75
    Conserved Domains (7) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    cd15714
    Location:798 → 907
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    pfam11725
    Location:475 → 671
    AvrE; Pathogenicity factor
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    cd20464
    Location:920 → 973
    Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
    cl02573
    Location:977 → 1032
    Tudor_SF; Tudor domain superfamily
    cl22851
    Location:686 → 789
    PHD_SF; PHD finger superfamily

  4. XM_006244320.5 → XP_006244382.1  lysine-specific demethylase 4B isoform X4

    UniProtKB/TrEMBL
    A0A8I5ZWQ3
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:922 → 972
    TUDOR; Tudor domain
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    cl22851
    Location:798 → 907
    PHD_SF; PHD finger superfamily

  5. XM_006244319.5 → XP_006244381.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/TrEMBL
    A0A0G2JXG2
    Related
    ENSRNOP00000070258.3, ENSRNOT00000089374.3
    Conserved Domains (5) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:888 → 938
    TUDOR; Tudor domain
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    cd15714
    Location:764 → 873
    ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
    cl22851
    Location:652 → 755
    PHD_SF; PHD finger superfamily

  6. XM_063266827.1 → XP_063122897.1  lysine-specific demethylase 4B isoform X3

    UniProtKB/TrEMBL
    A0A0G2JXG2

  7. XM_039083144.2 → XP_038939072.1  lysine-specific demethylase 4B isoform X5

    Conserved Domains (5) summary
    pfam11725
    Location:233 → 429
    AvrE; Pathogenicity factor
    cd20464
    Location:678 → 731
    Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
    cl02573
    Location:735 → 790
    Tudor_SF; Tudor domain superfamily
    cl22851
    Location:556 → 665
    PHD_SF; PHD finger superfamily
    cl40423
    Location:1 → 50
    cupin_RmlC-like; RmlC-like cupin superfamily

RNA

  1. XR_010054572.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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