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

Gene ID: 317432, updated on 2-May-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
Ensembl: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 histone H3-methyl-lysine-4 demethylase activity and zinc ion binding activity. Involved in response to toxic substance. Predicted to be located in cytosol and nucleoplasm. Biomarker of schizophrenia. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Claes-Jensen type. Orthologous to human KDM5C (lysine demethylase 5C). [provided by Alliance of Genome Resources, Apr 2022]
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. 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
  2. Impact of Patient Age on Molecular Alterations of Left-Sided Colorectal Tumors. Puccini A, et al. Oncologist, 2019 Mar. PMID 30018131, 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 (19) 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 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 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 response to toxic substance IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
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
  
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
    ENSRNOP00000071836.2, ENSRNOT00000079909.2

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

  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
    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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