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

Gene ID: 108829, updated on 12-Aug-2019

Summary

Official Symbol
Jmjd1cprovided by MGI
Official Full Name
jumonji domain containing 1Cprovided by MGI
Primary source
MGI:MGI:1918614
See related
Ensembl:ENSMUSG00000037876
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
Expression
Ubiquitous expression in cerebellum adult (RPKM 6.3), CNS E14 (RPKM 5.6) and 28 other tissues See more
Orthologs

Genomic context

See Jmjd1c in Genome Data Viewer
Location:
10; 10 B5.1
Exon count:
31
Annotation release Status Assembly Chr Location
108 current GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (67096351..67256326)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (66590006..66719074)

Chromosome 10 - NC_000076.6Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1110002J07 gene Neighboring gene VISTA enhancer mm1692 Neighboring gene predicted gene, 31763 Neighboring gene receptor accessory protein 3 Neighboring gene predicted gene, 46228 Neighboring gene U6 spliceosomal RNA 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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
epithelial cell morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone H3-K9 demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
maintenance of cell number IMP
Inferred from Mutant Phenotype
more info
PubMed 
male germ-line stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
male gonad development IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
reproductive senescence IMP
Inferred from Mutant Phenotype
more info
PubMed 
seminiferous tubule development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
probable JmjC domain-containing histone demethylation protein 2C
Names
jumonji domain-containing protein 1C

NCBI Reference Sequences (RefSeq)

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
    Related
    ENSMUSP00000133700.1, ENSMUST00000173689.7
    Conserved Domains (2) summary
    smart00558
    Location:21062160
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:21922291
    cupin_like; Conserved domain found in cupin and related proteins
  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
    ENSMUSP00000056227.9, ENSMUST00000051446.15
    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 108 details...Open this link in a new tab

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

Reference GRCm38.p6 C57BL/6J

Genomic

  1. NC_000076.6 Reference GRCm38.p6 C57BL/6J

    Range
    67096351..67256326
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030244815.1XP_030100675.1  probable JmjC domain-containing histone demethylation protein 2C isoform X10

  2. XM_006513042.4XP_006513105.1  probable JmjC domain-containing histone demethylation protein 2C isoform X11

    See identical proteins and their annotated locations for XP_006513105.1

    UniProtKB/Swiss-Prot
    Q69ZK6
    Conserved Domains (2) summary
    smart00558
    Location:21062160
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:21922291
    cupin_like; Conserved domain found in cupin and related proteins
  3. XM_030244806.1XP_030100666.1  probable JmjC domain-containing histone demethylation protein 2C isoform X7

  4. XM_006513044.4XP_006513107.1  probable JmjC domain-containing histone demethylation protein 2C isoform X10

    Conserved Domains (2) summary
    smart00558
    Location:20002054
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:20862185
    cupin_like; Conserved domain found in cupin and related proteins
  5. XM_030244816.1XP_030100676.1  probable JmjC domain-containing histone demethylation protein 2C isoform X10

  6. XM_030244807.1XP_030100667.1  probable JmjC domain-containing histone demethylation protein 2C isoform X8

  7. XM_030244812.1XP_030100672.1  probable JmjC domain-containing histone demethylation protein 2C isoform X9

  8. XM_030244805.1XP_030100665.1  probable JmjC domain-containing histone demethylation protein 2C isoform X11

  9. XM_030244814.1XP_030100674.1  probable JmjC domain-containing histone demethylation protein 2C isoform X9

  10. XM_030244817.1XP_030100677.1  probable JmjC domain-containing histone demethylation protein 2C isoform X10

  11. XM_030244810.1XP_030100670.1  probable JmjC domain-containing histone demethylation protein 2C isoform X8

  12. XM_006513041.3XP_006513104.1  probable JmjC domain-containing histone demethylation protein 2C isoform X11

    See identical proteins and their annotated locations for XP_006513104.1

    UniProtKB/Swiss-Prot
    Q69ZK6
    Conserved Domains (2) summary
    smart00558
    Location:21062160
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:21922291
    cupin_like; Conserved domain found in cupin and related proteins
  13. XM_006513035.4XP_006513098.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

    UniProtKB/TrEMBL
    G3UZM1
    Related
    ENSMUSP00000134551.1, ENSMUST00000174408.7
    Conserved Domains (2) summary
    smart00558
    Location:22872341
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:23732472
    cupin_like; Conserved domain found in cupin and related proteins
  14. XM_006513036.4XP_006513099.1  probable JmjC domain-containing histone demethylation protein 2C isoform X2

    Conserved Domains (2) summary
    smart00558
    Location:22622316
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:23482447
    cupin_like; Conserved domain found in cupin and related proteins
  15. XM_006513040.4XP_006513103.1  probable JmjC domain-containing histone demethylation protein 2C isoform X6

    Conserved Domains (2) summary
    smart00558
    Location:22192273
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:23052404
    cupin_like; Conserved domain found in cupin and related proteins
  16. XM_006513037.4XP_006513100.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

    Conserved Domains (2) summary
    smart00558
    Location:22492303
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:23352434
    cupin_like; Conserved domain found in cupin and related proteins
  17. XM_006513039.4XP_006513102.1  probable JmjC domain-containing histone demethylation protein 2C isoform X5

    Conserved Domains (2) summary
    smart00558
    Location:22872341
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:23732458
    cupin_like; Conserved domain found in cupin and related proteins
  18. XM_006513038.4XP_006513101.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

    Conserved Domains (2) summary
    smart00558
    Location:22872341
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:23732469
    cupin_like; Conserved domain found in cupin and related proteins
  19. XM_030244811.1XP_030100671.1  probable JmjC domain-containing histone demethylation protein 2C isoform X8

  20. XM_030244804.1XP_030100664.1  probable JmjC domain-containing histone demethylation protein 2C isoform X11

  21. XM_030244808.1XP_030100668.1  probable JmjC domain-containing histone demethylation protein 2C isoform X8

  22. XM_030244818.1XP_030100678.1  probable JmjC domain-containing histone demethylation protein 2C isoform X10

  23. XM_030244813.1XP_030100673.1  probable JmjC domain-containing histone demethylation protein 2C isoform X9

  24. XM_030244809.1XP_030100669.1  probable JmjC domain-containing histone demethylation protein 2C isoform X8

RNA

  1. XR_001779409.2 RNA Sequence

  2. XR_001779410.2 RNA Sequence

  3. XR_001779408.2 RNA Sequence

Reference GRCm38.p6 PATCHES

Genomic

  1. NW_019168511.1 Reference GRCm38.p6 PATCHES

    Range
    1535..28013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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