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

Gene ID: 108829, updated on 26-Sep-2022

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 H3-methyl-lysine-9 demethylase activity; and transcription coregulator activity. Acts upstream of or within several processes, including male germ-line stem cell population maintenance; reproductive senescence; and seminiferous tubule development. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex. Predicted to be active in chromatin. 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, Apr 2022]
Expression
Ubiquitous expression in cerebellum adult (RPKM 6.3), CNS E14 (RPKM 5.6) and 28 other tissues See more
Orthologs
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Genomic context

See Jmjd1c in Genome Data Viewer
Location:
10; 10 B5.1
Exon count:
31
Annotation release Status Assembly Chr Location
109 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 predicted gene, 53603 Neighboring gene VISTA enhancer mm1692 Neighboring gene predicted gene, 31763 Neighboring gene receptor accessory protein 3 Neighboring gene predicted gene, 26359 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)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of histone deacetylase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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

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_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
    Q69ZK6, 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: 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_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
    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
    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
    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
    Q69ZK6, 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
    Q69ZK6, 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
    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