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    Jmjd1c jumonji domain containing 1C [ Rattus norvegicus (Norway rat) ]

    Gene ID: 171120, updated on 14-Nov-2024

    Summary

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    Official Symbol
    Jmjd1cprovided by RGD
    Official Full Name
    jumonji domain containing 1Cprovided by RGD
    Primary source
    RGD:708458
    See related
    EnsemblRapid:ENSRNOG00000000648 AllianceGenome:RGD:708458
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Pr2
    Summary
    Predicted to enable chromatin DNA binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within epithelial cell morphogenesis; male germ-line stem cell population maintenance; and seminiferous tubule development. Predicted to be located in chromatin. Predicted to be part of histone deacetylase complex. Orthologous to human JMJD1C (jumonji domain containing 1C). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 260.8), Lung (RPKM 242.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Jmjd1c in Genome Data Viewer
    Location:
    20p11
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (21330990..21508580, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (21332147..21494220, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (22751743..22914080, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120098947 Neighboring gene U6 spliceosomal RNA Neighboring gene nuclear receptor binding factor 2 Neighboring gene receptor accessory protein 3 Neighboring gene uncharacterized LOC120098841 Neighboring gene uncharacterized LOC134483795

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Inhibition of histone demethylase JMJD1C attenuates cardiac hypertrophy and fibrosis induced by angiotensin II.
      Title: Inhibition of histone demethylase JMJD1C attenuates cardiac hypertrophy and fibrosis induced by angiotensin II.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within epithelial cell morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within maintenance of cell number ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within male germ-line stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within male gonad development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within seminiferous tubule development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    probable JmjC domain-containing histone demethylation protein 2C
    NP_001178648.3
    XP_006256421.2
    XP_006256422.2
    XP_006256423.1
    XP_006256424.1
    XP_006256426.1
    XP_038954331.1
    XP_038954333.1
    XP_063135015.1

    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_001191719.3 → NP_001178648.3  probable JmjC domain-containing histone demethylation protein 2C

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      A0A8I6ANV7
      Conserved Domains (3) summary
      smart00558
      Location:2263 → 2335
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl36576
      Location:126 → 174
      RX-CC_like; Coiled-coil domain of the potato virux X resistance protein and similar proteins
      cl40423
      Location:2367 → 2466
      cupin_RmlC-like; RmlC-like cupin 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_086038.1 Reference GRCr8

      Range
      21330990..21508580 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006256361.5 → XP_006256423.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

      See identical proteins and their annotated locations for XP_006256423.1

      UniProtKB/TrEMBL
      A0A8I6ANV7
      Conserved Domains (2) summary
      smart00558
      Location:2083 → 2155
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:2187 → 2286
      cupin_RmlC-like; RmlC-like cupin superfamily

    2. XM_006256362.5 → XP_006256424.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

      See identical proteins and their annotated locations for XP_006256424.1

      UniProtKB/TrEMBL
      A0A8I6ANV7
      Conserved Domains (2) summary
      smart00558
      Location:2083 → 2155
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:2187 → 2286
      cupin_RmlC-like; RmlC-like cupin superfamily

    3. XM_006256360.5 → XP_006256422.2  probable JmjC domain-containing histone demethylation protein 2C isoform X2

      UniProtKB/TrEMBL
      F1LMK8
      Related
      ENSRNOP00000094959.2, ENSRNOT00000109730.2
      Conserved Domains (3) summary
      smart00558
      Location:2196 → 2268
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl36576
      Location:126 → 174
      RX-CC_like; Coiled-coil domain of the potato virux X resistance protein and similar proteins
      cl40423
      Location:2300 → 2399
      cupin_RmlC-like; RmlC-like cupin superfamily

    4. XM_006256359.5 → XP_006256421.2  probable JmjC domain-containing histone demethylation protein 2C isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZN85, A0A8I6ANV7
      Related
      ENSRNOP00000079482.1, ENSRNOT00000099911.2
      Conserved Domains (3) summary
      smart00558
      Location:2264 → 2336
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl36576
      Location:126 → 174
      RX-CC_like; Coiled-coil domain of the potato virux X resistance protein and similar proteins
      cl40423
      Location:2368 → 2467
      cupin_RmlC-like; RmlC-like cupin superfamily

    5. XM_039098405.2 → XP_038954333.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

      UniProtKB/TrEMBL
      A0A8I6ANV7
      Conserved Domains (2) summary
      smart00558
      Location:2083 → 2155
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:2187 → 2286
      cupin_RmlC-like; RmlC-like cupin superfamily

    6. XM_039098403.2 → XP_038954331.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

      UniProtKB/TrEMBL
      A0A8I6ANV7
      Conserved Domains (2) summary
      smart00558
      Location:2083 → 2155
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:2187 → 2286
      cupin_RmlC-like; RmlC-like cupin superfamily

    7. XM_063278945.1 → XP_063135015.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

    8. XM_006256364.3 → XP_006256426.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      See identical proteins and their annotated locations for XP_006256426.1

      UniProtKB/TrEMBL
      F1LMK8
      Conserved Domains (2) summary
      smart00558
      Location:1977 → 2049
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:2081 → 2180
      cupin_like; Conserved domain found in cupin and related proteins

    RNA

    1. XR_010060624.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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