U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Jmjd1c jumonji domain containing 1C [ Mus musculus (house mouse) ]

    Gene ID: 108829, updated on 27-Nov-2024

    Summary

    Official Symbol
    Jmjd1cprovided by MGI
    Official Full Name
    jumonji domain containing 1Cprovided by MGI
    Primary source
    MGI:MGI:1918614
    See related
    Ensembl:ENSMUSG00000037876 AllianceGenome:MGI:1918614
    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
    TRIP8; Jmjdic; 5430433L24Rik; D630035I23Rik
    Summary
    Predicted to enable chromatin DNA binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Acts 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. Is expressed in several structures, including central nervous system; genitourinary system; heart; inner ear; and limb. Orthologous to human JMJD1C (jumonji domain containing 1C). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in cerebellum adult (RPKM 6.3), CNS E14 (RPKM 5.6) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Jmjd1c in Genome Data Viewer
    Location:
    10 B5.1; 10 34.85 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (66932189..67092105)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (67096351..67256326)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_26976 Neighboring gene predicted gene, 53603 Neighboring gene STARR-seq mESC enhancer starr_26978 Neighboring gene VISTA enhancer mm1692 Neighboring gene STARR-seq mESC enhancer starr_26980 Neighboring gene STARR-seq mESC enhancer starr_26981 Neighboring gene predicted gene, 31763 Neighboring gene receptor accessory protein 3 Neighboring gene STARR-positive B cell enhancer mm9_chr10:66531454-66531755 Neighboring gene STARR-positive B cell enhancer ABC_E8340 Neighboring gene STARR-seq mESC enhancer starr_26991 Neighboring gene STARR-seq mESC enhancer starr_26992 Neighboring gene STARR-positive B cell enhancer ABC_E10618 Neighboring gene predicted gene, 26359 Neighboring gene STARR-seq mESC enhancer starr_26997 Neighboring gene STARR-seq mESC enhancer starr_26998 Neighboring gene nuclear receptor binding factor 2 Neighboring gene predicted gene, 46200

    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)
    • Endonuclease-mediated (2) 
    • Targeted (4)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Gene Ontology Provided by MGI

    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 histone H3K9 demethylase activity IEA
    Inferred from Electronic Annotation
    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
     
    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
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    probable JmjC domain-containing histone demethylation protein 2C
    Names
    jumonji domain-containing protein 1C
    NP_001229325.1
    NP_997104.2
    XP_006513098.1
    XP_006513100.1
    XP_006513103.1
    XP_006513104.1
    XP_006513105.1
    XP_006513107.1
    XP_030100665.1
    XP_030100667.1
    XP_030100670.1
    XP_030100671.1
    XP_030100672.1
    XP_030100674.1
    XP_030100677.1
    XP_036011379.1
    XP_036011380.1
    XP_036011381.1
    XP_036011382.1
    XP_036011383.1
    XP_036011384.1
    XP_036011385.1
    XP_036011386.1
    XP_036011387.1
    XP_036011388.1

    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_001242396.1NP_001229325.1  probable JmjC domain-containing histone demethylation protein 2C isoform 2

      See identical proteins and their annotated locations for NP_001229325.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus and lacks a single internal aa compared to isoform 1.
      Source sequence(s)
      AC155712, AC156272, AK082106, AK085500, BC054559, BP761712, CD578529
      Consensus CDS
      CCDS56708.1
      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Related
      ENSMUSP00000133700.2, ENSMUST00000173689.8
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    2. NM_207221.3NP_997104.2  probable JmjC domain-containing histone demethylation protein 2C isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC155712, AC156272
      Consensus CDS
      CCDS56707.1
      UniProtKB/TrEMBL
      A0A0A0MQ98
      Related
      ENSMUSP00000056227.10, ENSMUST00000051446.16
      Conserved Domains (2) summary
      smart00558
      Location:22862340
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:23722471
      cupin_like; Conserved domain found in cupin and related proteins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      66932189..67092105
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036155486.1XP_036011379.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    2. XM_036155494.1XP_036011387.1  probable JmjC domain-containing histone demethylation protein 2C isoform X7

      Conserved Domains (3) summary
      smart00558
      Location:20002054
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:779973
      AvrE; Pathogenicity factor
      cl40423
      Location:20862185
      cupin_RmlC-like; RmlC-like cupin superfamily
    3. XM_036155489.1XP_036011382.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

      Conserved Domains (3) summary
      smart00558
      Location:20522106
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8311025
      AvrE; Pathogenicity factor
      cl40423
      Location:21382237
      cupin_RmlC-like; RmlC-like cupin superfamily
    4. XM_036155492.1XP_036011385.1  probable JmjC domain-containing histone demethylation protein 2C isoform X6

      Conserved Domains (3) summary
      smart00558
      Location:20382092
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8171011
      AvrE; Pathogenicity factor
      cl40423
      Location:21242223
      cupin_RmlC-like; RmlC-like cupin superfamily
    5. XM_036155487.1XP_036011380.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    6. XM_036155490.1XP_036011383.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

      Conserved Domains (3) summary
      smart00558
      Location:20522106
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8311025
      AvrE; Pathogenicity factor
      cl40423
      Location:21382237
      cupin_RmlC-like; RmlC-like cupin superfamily
    7. XM_036155493.1XP_036011386.1  probable JmjC domain-containing histone demethylation protein 2C isoform X6

      Conserved Domains (3) summary
      smart00558
      Location:20382092
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8171011
      AvrE; Pathogenicity factor
      cl40423
      Location:21242223
      cupin_RmlC-like; RmlC-like cupin superfamily
    8. XM_030244805.2XP_030100665.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    9. XM_030244817.2XP_030100677.1  probable JmjC domain-containing histone demethylation protein 2C isoform X7

      Conserved Domains (3) summary
      smart00558
      Location:20002054
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:779973
      AvrE; Pathogenicity factor
      cl40423
      Location:20862185
      cupin_RmlC-like; RmlC-like cupin superfamily
    10. XM_030244810.2XP_030100670.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

      Conserved Domains (3) summary
      smart00558
      Location:20522106
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8311025
      AvrE; Pathogenicity factor
      cl40423
      Location:21382237
      cupin_RmlC-like; RmlC-like cupin superfamily
    11. XM_030244814.2XP_030100674.1  probable JmjC domain-containing histone demethylation protein 2C isoform X6

      Conserved Domains (3) summary
      smart00558
      Location:20382092
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8171011
      AvrE; Pathogenicity factor
      cl40423
      Location:21242223
      cupin_RmlC-like; RmlC-like cupin superfamily
    12. XM_006513042.5XP_006513105.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      See identical proteins and their annotated locations for XP_006513105.1

      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    13. XM_006513044.5XP_006513107.1  probable JmjC domain-containing histone demethylation protein 2C isoform X7

      Conserved Domains (3) summary
      smart00558
      Location:20002054
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:779973
      AvrE; Pathogenicity factor
      cl40423
      Location:20862185
      cupin_RmlC-like; RmlC-like cupin superfamily
    14. XM_030244807.2XP_030100667.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

      Conserved Domains (3) summary
      smart00558
      Location:20522106
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8311025
      AvrE; Pathogenicity factor
      cl40423
      Location:21382237
      cupin_RmlC-like; RmlC-like cupin superfamily
    15. XM_030244812.2XP_030100672.1  probable JmjC domain-containing histone demethylation protein 2C isoform X6

      Conserved Domains (3) summary
      smart00558
      Location:20382092
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8171011
      AvrE; Pathogenicity factor
      cl40423
      Location:21242223
      cupin_RmlC-like; RmlC-like cupin superfamily
    16. XM_006513041.4XP_006513104.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      See identical proteins and their annotated locations for XP_006513104.1

      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    17. XM_036155491.1XP_036011384.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

      Conserved Domains (3) summary
      smart00558
      Location:20522106
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8311025
      AvrE; Pathogenicity factor
      cl40423
      Location:21382237
      cupin_RmlC-like; RmlC-like cupin superfamily
    18. XM_036155488.1XP_036011381.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

      UniProtKB/Swiss-Prot
      E9QMM8, Q69ZK6, Q6NV48, Q8BUF5, Q8C4I5, Q8C5Q9
      Conserved Domains (3) summary
      smart00558
      Location:21062160
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8851079
      AvrE; Pathogenicity factor
      cl40423
      Location:21922291
      cupin_RmlC-like; RmlC-like cupin superfamily
    19. XM_006513035.4XP_006513098.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

      UniProtKB/TrEMBL
      G3UZM1
      Related
      ENSMUSP00000134551.2, ENSMUST00000174408.8
      Conserved Domains (3) summary
      smart00558
      Location:22872341
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:10661260
      AvrE; Pathogenicity factor
      cl21464
      Location:23732472
      cupin_like; Conserved domain found in cupin and related proteins
    20. XM_006513040.4XP_006513103.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

      Conserved Domains (3) summary
      smart00558
      Location:22192273
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:9981192
      AvrE; Pathogenicity factor
      cl21464
      Location:23052404
      cupin_like; Conserved domain found in cupin and related proteins
    21. XM_006513037.4XP_006513100.1  probable JmjC domain-containing histone demethylation protein 2C isoform X2

      Conserved Domains (3) summary
      smart00558
      Location:22492303
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:10281222
      AvrE; Pathogenicity factor
      cl21464
      Location:23352434
      cupin_like; Conserved domain found in cupin and related proteins
    22. XM_030244811.1XP_030100671.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

      Conserved Domains (3) summary
      smart00558
      Location:20522106
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:8311025
      AvrE; Pathogenicity factor
      cl40423
      Location:21382237
      cupin_RmlC-like; RmlC-like cupin superfamily
    23. XM_036155495.1XP_036011388.1  probable JmjC domain-containing histone demethylation protein 2C isoform X7

      Conserved Domains (3) summary
      smart00558
      Location:20002054
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam11725
      Location:779973
      AvrE; Pathogenicity factor
      cl40423
      Location:20862185
      cupin_RmlC-like; RmlC-like cupin superfamily

    RNA

    1. XR_001779409.2 RNA Sequence

    2. XR_001779410.2 RNA Sequence

    3. XR_001779408.2 RNA Sequence

    4. XR_004936032.1 RNA Sequence