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

    Gene ID: 298144, updated on 9-Dec-2024

    Summary

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    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, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 158.7), Lung (RPKM 125.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    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

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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. 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

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    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

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    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)

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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_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

      UniProtKB/TrEMBL
      F1LS62

    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

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