U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Kdm4c lysine demethylase 4C [ Rattus norvegicus (Norway rat) ]

Gene ID: 298144, updated on 14-Nov-2024

Summary

Go to the top of the page Help
Symbol
Kdm4cprovided by RGD
Full Name
lysine demethylase 4Cprovided by RGD
Primary source
RGD:1307528
See related
EnsemblRapid:ENSRNOG00000006644 AllianceGenome:RGD:1307528
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
Also known as
Jmjd2c
Summary
Enables chromatin binding activity. Involved in positive regulation of gene expression and positive regulation of neuron differentiation. Located in chromatin. Human ortholog(s) of this gene implicated in autistic disorder; breast cancer; carcinoma (multiple); head and neck cancer; and withdrawal disorder. Orthologous to human KDM4C (lysine demethylase 4C). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 158.7), Lung (RPKM 125.1) and 9 other tissues See more
Orthologs
human mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See Kdm4c in Genome Data Viewer
Location:
5q31
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (93146404..93353040)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (88100710..88306821)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (90800139..91012662)

Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene FERM domain containing 3 Neighboring gene COMM domain-containing protein 2 pseudogene Neighboring gene developmental pluripotency-associated 3, pseudogene 2 Neighboring gene protein kinase C iota type-like Neighboring gene ribosomal protein L9, pseudogene 24 Neighboring gene small nucleolar RNA SNORA17

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

Go to the top of the pageHelp

Related articles in PubMed

  1. MicroRNA-340-5p inhibits endothelial apoptosis, inflammatory response, and pro-coagulation by targeting KDM4C in anti-neutrophil cytoplasmic antibody (ANCA)-mediated glomerulonephritis through activation of B cells. Hu J, et al. Autoimmunity, 2021 Sep. PMID 34121556
  2. [Expressions of Jumonji domain containing protein 2C and hypoxia-inducible factor-1α in gastric carcinoma and their clinical significance]. Xu Y, et al. Zhonghua Yi Xue Za Zhi, 2013 Nov 12. PMID 24418035
  3. Histone demethylase GASC1, a potential prognostic and predictive marker in esophageal squamous cell carcinoma. Sun LL, et al. Am J Cancer Res, 2013. PMID 24224128, Free PMC Article
  4. Genome-wide association study in esophageal cancer using GeneChip mapping 10K array. Hu N, et al. Cancer Res, 2005 Apr 1. PMID 15805246
  5. Renal cell neoplasms contain shared tumor type-specific copy number variations. Krill-Burger JM, et al. Am J Pathol, 2012 Jun. PMID 22483639, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. MicroRNA-340-5p inhibits endothelial apoptosis, inflammatory response, and pro-coagulation by targeting KDM4C in anti-neutrophil cytoplasmic antibody (ANCA)-mediated glomerulonephritis through activation of B cells.
    Title: MicroRNA-340-5p inhibits endothelial apoptosis, inflammatory response, and pro-coagulation by targeting KDM4C in anti-neutrophil cytoplasmic antibody (ANCA)-mediated glomerulonephritis through activation of B cells.
  2. Data indicate that histone demethylases KDM4A/C regulate H3K9 and H3K36 methylation on brain-derived neurotrophic factor (BDNF) versus astroglial glial fibrillary acidic protein (GFAP) genes in neural stem cells.
    Title: Gene-specific methylation control of H3K9 and H3K36 on neurotrophic BDNF versus astroglial GFAP genes by KDM4A/C regulates neural stem cell differentiation.
Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K36 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 nuclear androgen receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables nuclear receptor coactivator activity ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in androgen receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within blastocyst formation ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of stem cell differentiation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within stem cell population maintenance ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromatin ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in pericentric heterochromatin ISO
Inferred from Sequence Orthology
more info
  

General protein information

Go to the top of the page Help
Preferred Names
lysine-specific demethylase 4C
Names
jumonji domain containing 2C
lysine (K)-specific demethylase 4C
lysine-specific demethylase 4C-like
NP_001100133.3
XP_038965424.1
XP_038965425.1
XP_038965426.1
XP_038965427.1
XP_038965428.1
XP_038965430.1
XP_038965431.1
XP_063143431.1
XP_063143432.1
XP_063143433.1
XP_063143434.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_001106663.4 → NP_001100133.3  lysine-specific demethylase 4C

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000005
    UniProtKB/TrEMBL
    F1LS62
    Related
    ENSRNOP00000009083.9, ENSRNOT00000009083.10
    Conserved Domains (4) summary
    smart00333
    Location:874 → 930
    TUDOR; Tudor domain
    pfam02373
    Location:177 → 293
    JmjC; JmjC domain, hydroxylase
    cl15840
    Location:16 → 57
    JmjN; jmjN domain
    cl22851
    Location:752 → 861
    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_086023.1 Reference GRCr8

    Range
    93146404..93353040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063287361.1 → XP_063143431.1  lysine-specific demethylase 4C isoform X3

  2. XM_063287364.1 → XP_063143434.1  lysine-specific demethylase 4C isoform X8

  3. XM_039109496.2 → XP_038965424.1  lysine-specific demethylase 4C isoform X1

    UniProtKB/TrEMBL
    A0A8I6A8Y8, F1LS62
    Conserved Domains (5) summary
    pfam02373
    Location:177 → 293
    JmjC; JmjC domain, hydroxylase
    cd20465
    Location:832 → 885
    Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cd20468
    Location:889 → 948
    Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cl15840
    Location:16 → 57
    JmjN; jmjN domain
    cl22851
    Location:708 → 817
    PHD_SF; PHD finger superfamily

  4. XM_039109502.2 → XP_038965430.1  lysine-specific demethylase 4C isoform X5

    UniProtKB/TrEMBL
    A6J816
    Conserved Domains (3) summary
    pfam02373
    Location:177 → 293
    JmjC; JmjC domain, hydroxylase
    pfam02375
    Location:17 → 51
    JmjN; jmjN domain
    cl22851
    Location:642 → 743
    PHD_SF; PHD finger superfamily

  5. XM_063287363.1 → XP_063143433.1  lysine-specific demethylase 4C isoform X7

    UniProtKB/TrEMBL
    B0BNJ6

  6. XM_039109498.2 → XP_038965426.1  lysine-specific demethylase 4C isoform X2

    UniProtKB/TrEMBL
    A0A8I6A3B2, F1LS62
    Conserved Domains (4) summary
    pfam02373
    Location:102 → 218
    JmjC; JmjC domain, hydroxylase
    cd20465
    Location:801 → 854
    Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cd20468
    Location:858 → 917
    Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cl22851
    Location:677 → 786
    PHD_SF; PHD finger superfamily

  7. XM_039109499.2 → XP_038965427.1  lysine-specific demethylase 4C isoform X4

    UniProtKB/TrEMBL
    F1LS62
    Related
    ENSRNOP00000088229.2, ENSRNOT00000110293.2
    Conserved Domains (4) summary
    pfam02373
    Location:1 → 112
    JmjC; JmjC domain, hydroxylase
    cd20465
    Location:695 → 748
    Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cd20468
    Location:752 → 811
    Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cl22851
    Location:571 → 680
    PHD_SF; PHD finger superfamily

  8. XM_039109497.2 → XP_038965425.1  lysine-specific demethylase 4C isoform X2

    UniProtKB/TrEMBL
    A0A8I6A3B2, F1LS62
    Conserved Domains (4) summary
    pfam02373
    Location:102 → 218
    JmjC; JmjC domain, hydroxylase
    cd20465
    Location:801 → 854
    Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cd20468
    Location:858 → 917
    Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cl22851
    Location:677 → 786
    PHD_SF; PHD finger superfamily

  9. XM_039109500.2 → XP_038965428.1  lysine-specific demethylase 4C isoform X4

    UniProtKB/TrEMBL
    F1LS62
    Conserved Domains (4) summary
    pfam02373
    Location:1 → 112
    JmjC; JmjC domain, hydroxylase
    cd20465
    Location:695 → 748
    Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cd20468
    Location:752 → 811
    Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cl22851
    Location:571 → 680
    PHD_SF; PHD finger superfamily

  10. XM_039109503.2 → XP_038965431.1  lysine-specific demethylase 4C isoform X6

    Conserved Domains (3) summary
    cd20465
    Location:563 → 616
    Tudor_JMJD2C_rpt1; first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cd20468
    Location:620 → 679
    Tudor_JMJD2C_rpt2; second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins
    cl22851
    Location:439 → 548
    PHD_SF; PHD finger superfamily

  11. XM_063287362.1 → XP_063143432.1  lysine-specific demethylase 4C isoform X6

RNA

  1. XR_010066353.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools