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    Kdm5c lysine (K)-specific demethylase 5C [ Mus musculus (house mouse) ]

    Gene ID: 20591, updated on 22-Aug-2021

    Summary

    Official Symbol
    Kdm5cprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 5Cprovided by MGI
    Primary source
    MGI:MGI:99781
    See related
    Ensembl:ENSMUSG00000025332
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Smc; Jari; Smcx; Jarid1c; mKIAA0234; D930009K15Rik
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 13.0), ovary adult (RPKM 12.8) and 28 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Kdm5c in Genome Data Viewer
    Location:
    X F3; X 68.46 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) X NC_000086.8 (151015698..151062098)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (152233198..152279102)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) X NC_000086.6 (148667773..148708897)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain 2 Neighboring gene predicted gene, 52480 Neighboring gene predicted gene, 52430 Neighboring gene Kdm5c adjacent non-coding transcript Neighboring gene TSPY-like 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    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 H3-methyl-lysine-4 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3-tri/di/monomethyl-lysine-4 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    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
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 5C
    Names
    [histone H3]-trimethyl-L-lysine(4) demethylase 5C
    histone demethylase JARID1C
    jumonji, AT rich interactive domain 1C (Rbp2 like)
    jumonji/ARID domain-containing protein 1C
    selected mouse cDNA on the X
    NP_038696.2
    XP_006528832.1
    XP_006528833.1
    XP_006528834.1
    XP_006528835.1
    XP_006528836.1
    XP_017173931.1
    XP_017173932.1
    XP_030107134.1
    XP_036017763.1

    NCBI Reference Sequences (RefSeq)

    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_013668.4NP_038696.2  lysine-specific demethylase 5C

      Status: VALIDATED

      Source sequence(s)
      AC083816, AI553515, AK150152, AK155651, BC043096
      Consensus CDS
      CCDS41178.1
      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000108207.3, ENSMUST00000112588.9
      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11871247
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000086.8 Reference GRCm39 C57BL/6J

      Range
      151015698..151062098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528769.5XP_006528832.1  lysine-specific demethylase 5C isoform X1

      See identical proteins and their annotated locations for XP_006528832.1

      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000108203.2, ENSMUST00000112584.8
      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:79170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11871247
      PHD_SF; PHD finger superfamily
    2. XM_017318443.3XP_017173932.1  lysine-specific demethylase 5C isoform X9

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:79170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11411201
      PHD_SF; PHD finger superfamily
    3. XM_017318442.3XP_017173931.1  lysine-specific demethylase 5C isoform X3

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:325370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:500616
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:79170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02928
      Location:706758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7711097
      PLU-1; PLU-1-like protein
      cl22851
      Location:11861246
      PHD_SF; PHD finger superfamily
    4. XM_006528772.5XP_006528835.1  lysine-specific demethylase 5C isoform X6

      See identical proteins and their annotated locations for XP_006528835.1

      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000080814.7, ENSMUST00000082177.13
      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:285330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:460576
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:68129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:666718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7311057
      PLU-1; PLU-1-like protein
      cl22851
      Location:11461206
      PHD_SF; PHD finger superfamily
    5. XM_006528773.5XP_006528836.1  lysine-specific demethylase 5C isoform X8

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:326371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:501617
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:79170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02928
      Location:707759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7721098
      PLU-1; PLU-1-like protein
      cl22851
      Location:11411201
      PHD_SF; PHD finger superfamily
    6. XM_006528770.5XP_006528833.1  lysine-specific demethylase 5C isoform X2

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:325370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:500616
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:79170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02928
      Location:706758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7711097
      PLU-1; PLU-1-like protein
      cl22851
      Location:11861246
      PHD_SF; PHD finger superfamily
    7. XM_006528771.5XP_006528834.1  lysine-specific demethylase 5C isoform X4

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:285330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:460576
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:68129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:666718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7311057
      PLU-1; PLU-1-like protein
      cl22851
      Location:11461206
      PHD_SF; PHD finger superfamily
    8. XM_036161870.1XP_036017763.1  lysine-specific demethylase 5C isoform X7

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:284329
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cl28902
      Location:68129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02373
      Location:459575
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:665717
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7301056
      PLU-1; PLU-1-like protein
      cl22851
      Location:11451205
      PHD_SF; PHD finger superfamily
    9. XM_030251274.2XP_030107134.1  lysine-specific demethylase 5C isoform X5

      Conserved Domains (7) summary
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:284329
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:459575
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:68129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:665717
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7301056
      PLU-1; PLU-1-like protein
      cl22851
      Location:11451205
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_003953003.2 RNA Sequence

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