Human Gene JMJD1C (uc001jmm.3) Description and Page Index
  Description: Homo sapiens jumonji domain containing 1C (JMJD1C), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr10:64,926,988-65,028,982 Size: 101,995 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chr10:64,927,805-64,975,173 Size: 47,369 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:64,926,988-65,028,982)mRNA (may differ from genome)Protein (2252 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIneXtProtPubMed
ReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: JHD2C_HUMAN
DESCRIPTION: RecName: Full=Probable JmjC domain-containing histone demethylation protein 2C; EC=1.14.11.-; AltName: Full=Jumonji domain-containing protein 1C; AltName: Full=Thyroid receptor-interacting protein 8; Short=TR-interacting protein 8; Short=TRIP-8;
FUNCTION: Probable histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May be involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes (By similarity).
COFACTOR: Binds 1 Fe(2+) ion per subunit (By similarity).
SUBUNIT: Interacts specifically with the ligand-binding domain of the thyroid receptor (TR). Requires the presence of thyroid hormone for its interaction.
INTERACTION: P10275:AR; NbExp=2; IntAct=EBI-1224969, EBI-608057;
SUBCELLULAR LOCATION: Nucleus (By similarity).
DOMAIN: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the JHDM2 histone demethylase family.
SIMILARITY: Contains 1 JmjC domain.
SEQUENCE CAUTION: Sequence=AAC41741.1; Type=Frameshift; Positions=2171; Sequence=CAD97921.1; Type=Frameshift; Positions=1697; Sequence=CAI10947.1; Type=Erroneous gene model prediction;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): JMJD1C
CDC HuGE Published Literature: JMJD1C
Positive Disease Associations: Alkaline Phosphatase , C-Reactive Protein , Face , mean platelet volume , plasma levels of liver enzymes , Platelet Aggregation , Platelet Count , Triglycerides
Related Studies:
  1. Alkaline Phosphatase
    Xin Yuan et al. American journal of human genetics 2008, Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes., American journal of human genetics. [PubMed 18940312]
  2. Alkaline Phosphatase
    Xin Yuan et al. American journal of human genetics 2008, Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes., American journal of human genetics. [PubMed 18940312]
  3. Alkaline Phosphatase
    John C Chambers et al. Nature genetics 2011, Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma., Nature genetics. [PubMed 22001757]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: JMJD1C
Diseases sorted by gene-association score: central nervous system germinoma* (25), rett syndrome (9), velocardiofacial syndrome* (7), persistent hyperplastic primary vitreous (4), intellectual disability (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • C023514 2,6-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D016604 Aflatoxin B1
  • D000643 Ammonium Chloride
  • D017638 Asbestos, Crocidolite
  • D019256 Cadmium Chloride
  • D004237 Diuron
  • D005557 Formaldehyde
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.63 RPKM in Brain - Cerebellum
Total median expression: 364.75 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -317.901095-0.290 Picture PostScript Text
3' UTR -189.80817-0.232 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003347 - JmjC_dom

Pfam Domains:
PF02373 - JmjC domain, hydroxylase

SCOP Domains:
51197 - Clavaminate synthase-like

ModBase Predicted Comparative 3D Structure on Q15652
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000976 transcription regulatory region sequence-specific DNA binding
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0031490 chromatin DNA binding
GO:0032454 histone demethylase activity (H3-K9 specific)
GO:0046872 metal ion binding
GO:0046966 thyroid hormone receptor binding
GO:0051213 dioxygenase activity

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007596 blood coagulation
GO:0033169 histone H3-K9 demethylation
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0000785 chromatin
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  EF068222 - Homo sapiens jumonji domain-containing 1 C splice variant (JMJD1C) mRNA, complete cds, alternatively spliced.
BX537954 - Homo sapiens mRNA; cDNA DKFZp686K091 (from clone DKFZp686K091); complete cds.
BC126403 - Homo sapiens cDNA clone IMAGE:8992119, containing frame-shift errors.
BC143722 - Homo sapiens jumonji domain containing 1C, mRNA (cDNA clone MGC:177253 IMAGE:9052236), complete cds.
AK027280 - Homo sapiens cDNA FLJ14374 fis, clone HEMBA1001635.
BC108649 - Homo sapiens jumonji domain containing 1C, mRNA (cDNA clone IMAGE:6069106), with apparent retained intron.
AL831917 - Homo sapiens mRNA; cDNA DKFZp761F0118 (from clone DKFZp761F0118).
BC047331 - Homo sapiens jumonji domain containing 1C, mRNA (cDNA clone IMAGE:4456196), partial cds.
BC065742 - Homo sapiens jumonji domain containing 1C, mRNA (cDNA clone IMAGE:4702370).
BC037981 - Homo sapiens jumonji domain containing 1C, mRNA (cDNA clone IMAGE:5245966), with apparent retained intron.
AK123507 - Homo sapiens cDNA FLJ41513 fis, clone BRTHA2010191.
AB037801 - Homo sapiens mRNA for KIAA1380 protein, partial cds.
JD469834 - Sequence 450858 from Patent EP1572962.
JD229185 - Sequence 210209 from Patent EP1572962.
JD370718 - Sequence 351742 from Patent EP1572962.
BC156414 - Synthetic construct Homo sapiens clone IMAGE:100062940, MGC:190643 jumonji domain containing 1C (JMJD1C) mRNA, encodes complete protein.
AK024991 - Homo sapiens cDNA: FLJ21338 fis, clone COL02572.
L40411 - Homo sapiens thyroid receptor interactor (TRIP8) mRNA, 3' end of cds.
AK056660 - Homo sapiens cDNA FLJ32098 fis, clone OCBBF2001124, weakly similar to TESTIS SPECIFIC PROTEIN A.
AK095584 - Homo sapiens cDNA FLJ38265 fis, clone FCBBF3001855, weakly similar to Homo sapiens zinc finger protein mRNA.
BC026268 - Homo sapiens jumonji domain containing 1C, mRNA (cDNA clone IMAGE:4703438), partial cds.
AK126040 - Homo sapiens cDNA FLJ44052 fis, clone TESTI4033690.
JD528738 - Sequence 509762 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q15652 (Reactome details) participates in the following event(s):

R-HSA-997263 JMJD1C demethylates H3K9 mono- and di-methylation
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A0T124, BC126403, JHD2C_HUMAN, JHDM2C, KIAA1380, Q15652, Q5SQZ8, Q5SQZ9, Q5SR00, Q7Z3E7, Q8N3U0, Q96KB9, Q9P2G7, TRIP8
UCSC ID: uc001jmm.3
RefSeq Accession: NM_004241
Protein: Q15652 (aka JHD2C_HUMAN)
CCDS: CCDS60538.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC126403.1
exon count: 25CDS single in 3' UTR: no RNA size: 8161
ORF size: 6759CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 13304.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.