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JMJD1C jumonji domain containing 1C [ Homo sapiens (human) ]

Gene ID: 221037, updated on 8-Jan-2023

Summary

Official Symbol
JMJD1Cprovided by HGNC
Official Full Name
jumonji domain containing 1Cprovided by HGNC
Primary source
HGNC:HGNC:12313
See related
Ensembl:ENSG00000171988 MIM:604503; AllianceGenome:HGNC:12313
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KDM3C; TRIP8; TRIP-8
Summary
The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in bone marrow (RPKM 14.8), gall bladder (RPKM 12.0) and 25 other tissues See more
Orthologs
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Genomic context

See JMJD1C in Genome Data Viewer
Location:
10q21.3
Exon count:
33
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (63167225..63521890, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (64025342..64324116, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (64926985..65281650, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378328 Neighboring gene nuclear receptor binding factor 2 Neighboring gene TatD DNase domain containing 1 pseudogene 1 Neighboring gene uncharacterized LOC124900287 Neighboring gene microRNA 1296 Neighboring gene JMJD1C antisense RNA 2 Neighboring gene PRELID1 pseudogene 3 Neighboring gene JMJD1C antisense RNA 1 Neighboring gene receptor accessory protein 3 Neighboring gene Sharpr-MPRA regulatory region 5662 Neighboring gene uncharacterized LOC105378329

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
EBI GWAS Catalog
A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation.
EBI GWAS Catalog
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
EBI GWAS Catalog
A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.
EBI GWAS Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog
Genome-wide association analysis of juvenile idiopathic arthritis identifies a new susceptibility locus at chromosomal region 3q13.
EBI GWAS Catalog
Genome-wide association study identifies a new locus JMJD1C at 10q21 that may influence serum androgen levels in men.
EBI GWAS Catalog
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
EBI GWAS Catalog
Genome-wide association study indicates variants associated with insulin signaling and inflammation mediate lipoprotein responses to fenofibrate.
EBI GWAS Catalog
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
EBI GWAS Catalog
Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists.
EBI GWAS Catalog
GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
EBI GWAS Catalog
Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
EBI GWAS Catalog
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ14374, KIAA1380, DKFZp761F0118

Gene Ontology Provided by GOA

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 histone H3K9 demethylase activity TAS
Traceable Author Statement
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nuclear thyroid hormone receptor binding TAS
Traceable Author Statement
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in blood coagulation TAS
Traceable Author Statement
more info
 
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H3-K9 demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of DNA-templated transcription TAS
Traceable Author Statement
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II 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 nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
probable JmjC domain-containing histone demethylation protein 2C
Names
TR-interacting protein 8
thyroid hormone receptor interactor 8
thyroid receptor-interacting protein 8

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.

Genomic

  1. NG_053187.2 RefSeqGene

    Range
    60913..359665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282948.2NP_001269877.1  probable JmjC domain-containing histone demethylation protein 2C isoform c

    See identical proteins and their annotated locations for NP_001269877.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as s-JMJD1C) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AL590502, AL607128, AL713895
    Consensus CDS
    CCDS60538.1
    UniProtKB/Swiss-Prot
    Q15652
    UniProtKB/TrEMBL
    B7ZLC8
    Related
    ENSP00000444682.1, ENST00000542921.5
    Conserved Domains (3) summary
    smart00558
    Location:20962168
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam12067
    Location:546613
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:22002299
    cupin_like; Conserved domain found in cupin and related proteins
  2. NM_001318153.2NP_001305082.1  probable JmjC domain-containing histone demethylation protein 2C isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AL590502, AL607128, AL713895
    UniProtKB/Swiss-Prot
    Q15652
    Conserved Domains (3) summary
    smart00558
    Location:19902062
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam12067
    Location:440507
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:20942193
    cupin_like; Conserved domain found in cupin and related proteins
  3. NM_001318154.2NP_001305083.1  probable JmjC domain-containing histone demethylation protein 2C isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (c, also known as s-JMJD1C) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AC022022, AL590502, AL607128, AL713895
    Consensus CDS
    CCDS60538.1
    UniProtKB/Swiss-Prot
    Q15652
    Conserved Domains (3) summary
    smart00558
    Location:20962168
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam12067
    Location:546613
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:22002299
    cupin_like; Conserved domain found in cupin and related proteins
  4. NM_001322252.2NP_001309181.1  probable JmjC domain-containing histone demethylation protein 2C isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (e) that is shorter than isoform a.
    Source sequence(s)
    AC022022, AL590502, AL713895
    UniProtKB/Swiss-Prot
    Q15652
    Conserved Domains (3) summary
    smart00558
    Location:22402312
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam12067
    Location:690757
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:23442443
    cupin_like; Conserved domain found in cupin and related proteins
  5. NM_001322254.2NP_001309183.1  probable JmjC domain-containing histone demethylation protein 2C isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (f) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform f.
    Source sequence(s)
    AL590502, AL607128, AL713895
    UniProtKB/Swiss-Prot
    Q15652
    UniProtKB/TrEMBL
    B7ZLC8
    Conserved Domains (3) summary
    smart00558
    Location:20592131
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:21632262
    cupin_like; Conserved domain found in cupin and related proteins
    cl26511
    Location:88453
    Neuromodulin_N; Gap junction protein N-terminal region
  6. NM_001322258.2NP_001309187.1  probable JmjC domain-containing histone demethylation protein 2C isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (f) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform f.
    Source sequence(s)
    AC022022, AL590502, AL607128, AL713895
    UniProtKB/Swiss-Prot
    Q15652
    Conserved Domains (3) summary
    smart00558
    Location:20592131
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl21464
    Location:21632262
    cupin_like; Conserved domain found in cupin and related proteins
    cl26511
    Location:88453
    Neuromodulin_N; Gap junction protein N-terminal region
  7. NM_032776.3NP_116165.1  probable JmjC domain-containing histone demethylation protein 2C isoform a

    See identical proteins and their annotated locations for NP_116165.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC022022, AL590502, AL607128, AL713895
    Consensus CDS
    CCDS41532.1
    UniProtKB/Swiss-Prot
    Q15652, Q9P2G7
    Related
    ENSP00000382204.2, ENST00000399262.7
    Conserved Domains (4) summary
    smart00558
    Location:22782350
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cd14798
    Location:127175
    RX-CC_like; Coiled-coil domain of the potato virux X resistance protein and similar proteins
    pfam12067
    Location:728795
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:23822481
    cupin_like; Conserved domain found in cupin and related proteins

RNA

  1. NR_134512.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains alternate 5' exon structure, lacks two internal exons, and uses two alternate splice sites, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, which is in-frame with the coding sequence of variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL590502, AL607128, AL713895
    Related
    ENST00000402544.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    63167225..63521890 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017015897.2XP_016871386.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

    UniProtKB/Swiss-Prot
    Q15652
    Conserved Domains (3) summary
    smart00558
    Location:20962168
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam12067
    Location:546613
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:22002299
    cupin_like; Conserved domain found in cupin and related proteins
  2. XM_047424773.1XP_047280729.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

  3. XM_047424772.1XP_047280728.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

  4. XM_047424774.1XP_047280730.1  probable JmjC domain-containing histone demethylation protein 2C isoform X2

  5. XM_017015898.2XP_016871387.1  probable JmjC domain-containing histone demethylation protein 2C isoform X1

    UniProtKB/Swiss-Prot
    Q15652
    Conserved Domains (3) summary
    smart00558
    Location:20962168
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam12067
    Location:546613
    Sox_C_TAD; Sox C-terminal transactivation domain
    cl21464
    Location:22002299
    cupin_like; Conserved domain found in cupin and related proteins
  6. XM_047424775.1XP_047280731.1  probable JmjC domain-containing histone demethylation protein 2C isoform X3

  7. XM_011539508.3XP_011537810.1  probable JmjC domain-containing histone demethylation protein 2C isoform X4

    Conserved Domains (1) summary
    PTZ00121
    Location:125490
    PTZ00121; MAEBL; Provisional

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    64025342..64324116 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004241.2: Suppressed sequence

    Description
    NM_004241.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.