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    Kdm5c lysine demethylase 5C [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317432, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Kdm5cprovided by RGD
    Official Full Name
    lysine demethylase 5Cprovided by RGD
    Primary source
    RGD:1560601
    See related
    EnsemblRapid:ENSRNOG00000057706 AllianceGenome:RGD:1560601
    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
    RGD1560601
    Summary
    Predicted to enable several functions, including histone H3K4me/H3K4me2/H3K4me3 demethylase activity; identical protein binding activity; and zinc ion binding activity. Involved in response to toxic substance. Predicted to be located in chromatin; cytosol; and nucleoplasm. Predicted to be active in nucleus. Biomarker of schizophrenia. Human ortholog(s) of this gene implicated in descending colon cancer and syndromic X-linked intellectual disability Claes-Jensen type. Orthologous to human KDM5C (lysine demethylase 5C). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 184.2), Kidney (RPKM 174.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Kdm5c in Genome Data Viewer
    Location:
    Xq13
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (24821568..24866423)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (21345459..21387045)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (22302664..22349298)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene large ribosomal subunit protein eL31-like Neighboring gene IQ motif and Sec7 domain ArfGEF 2 Neighboring gene KANTR integral membrane protein Neighboring gene KANTR integral membrane protein

    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. Impact of Patient Age on Molecular Alterations of Left-Sided Colorectal Tumors. Puccini A, et al. Oncologist, 2019 Mar. PMID 30018131, Free PMC Article
    2. KDM5c Promotes Colon Cancer Cell Proliferation Through the FBXW7-c-Jun Regulatory Axis. Lin H, et al. Front Oncol, 2020. PMID 33042830, Free PMC Article
    3. A novel c.2T > C mutation of the KDM5C/JARID1C gene in one large family with X-linked intellectual disability. Ounap K, et al. Eur J Med Genet, 2012 Mar. PMID 22326837
    4. Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia. Abidi FE, et al. J Med Genet, 2008 Dec. PMID 18697827, Free PMC Article
    5. METTL14-mediated N6-methyladenosine modification of SOX4 mRNA inhibits tumor metastasis in colorectal cancer. Chen X, et al. Mol Cancer, 2020 Jun 17. PMID 32552762, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to toxic substance IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    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
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 5C
    Names
    lysine (K)-specific demethylase 5C
    NP_001406701.1
    XP_038956409.1
    XP_038956410.1
    XP_038956411.1
    XP_038956412.1
    XP_038956413.1
    XP_038956414.1
    XP_038956415.1
    XP_063136143.1
    XP_063136144.1
    XP_063136145.1

    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_001419772.1 → NP_001406701.1  lysine-specific demethylase 5C

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A0G2K1H0
      Related
      ENSRNOP00000111484.1, ENSRNOT00000146574.1

    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_086039.1 Reference GRCr8

      Range
      24821568..24866423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039100482.2 → XP_038956410.1  lysine-specific demethylase 5C isoform X2

      UniProtKB/TrEMBL
      V9GW19
      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd16875
      Location:79 → 170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein
      cl22851
      Location:1187 → 1247
      PHD_SF; PHD finger superfamily

    2. XM_039100486.2 → XP_038956414.1  lysine-specific demethylase 5C isoform X8

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd16875
      Location:79 → 170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein
      cl22851
      Location:1141 → 1201
      PHD_SF; PHD finger superfamily

    3. XM_063280075.1 → XP_063136145.1  lysine-specific demethylase 5C isoform X9

      Related
      ENSRNOP00000071836.3, ENSRNOT00000079909.3

    4. XM_039100481.2 → XP_038956409.1  lysine-specific demethylase 5C isoform X1

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd16875
      Location:79 → 170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein
      cl22851
      Location:1186 → 1246
      PHD_SF; PHD finger superfamily

    5. XM_039100483.2 → XP_038956411.1  lysine-specific demethylase 5C isoform X3

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd16875
      Location:79 → 170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1097
      PLU-1; PLU-1-like protein
      cl22851
      Location:1186 → 1246
      PHD_SF; PHD finger superfamily

    6. XM_039100484.2 → XP_038956412.1  lysine-specific demethylase 5C isoform X4

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:285 → 330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cl28902
      Location:68 → 129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02373
      Location:460 → 576
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:666 → 718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:731 → 1057
      PLU-1; PLU-1-like protein
      cl22851
      Location:1146 → 1206
      PHD_SF; PHD finger superfamily

    7. XM_039100485.2 → XP_038956413.1  lysine-specific demethylase 5C isoform X6

      UniProtKB/TrEMBL
      A0A0G2K897
      Related
      ENSRNOP00000074522.2, ENSRNOT00000082725.3
      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:285 → 330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cl28902
      Location:68 → 129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02373
      Location:460 → 576
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:666 → 718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:731 → 1057
      PLU-1; PLU-1-like protein
      cl22851
      Location:1146 → 1206
      PHD_SF; PHD finger superfamily

    8. XM_063280073.1 → XP_063136143.1  lysine-specific demethylase 5C isoform X5

    9. XM_063280074.1 → XP_063136144.1  lysine-specific demethylase 5C isoform X7

    10. XM_039100487.2 → XP_038956415.1  lysine-specific demethylase 5C isoform X10

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd16875
      Location:79 → 170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02373
      Location:501 → 617
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein
      cl22851
      Location:1187 → 1247
      PHD_SF; PHD finger superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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