Tbio JMJD1C Probable JmjC domain-containing histone demethylation protein 2C

Protein Classes

PANTHER Classes

Protein / Transcription Factor / Zinc Finger Transcription Factor / Probable Jmjc Domain-containing Histone Demethylation Protein 2C

Protein Summary

Description

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). 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]

Uniprot Accession IDs

• Q15652
• A0T124
• Q5SQZ8
• Q5SQZ9
• Q5SR00
• Q7Z3E7
• Q8N3U0
• Q96KB9
• Q9P2G7

Gene Name

• JMJD1C

Ensembl ID

• ENST00000399262
• ENSP00000382204
• ENSG00000171988
• ENST00000542921
• ENSP00000444682

Symbol

• JHDM2C
• KIAA1380
• TRIP8
• KDM3C
• TRIP8
• TRIP-8

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
histone modification site profile	0.87
trait	0.86
transcription factor	0.86
cell type or tissue	0.76
transcription factor binding site profile	0.76

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 37.84   (req: < 5)

Gene RIFs: 18   (req: <= 3)

Antibodies: 130   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 37.84   (req: >= 5)

Gene RIFs: 18   (req: > 3)

Antibodies: 130   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 9

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (59)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

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GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
sex hormone-binding globulin measurement	EFO_0004696	5	4	8		99.8
triglyceride measurement	EFO_0004530	12	9	17	3.1	99.1
self reported educational attainment	EFO_0004784	4	4	3	6.6	98.5
mean platelet volume	EFO_0004584	9	9	10		98.4
platelet count	EFO_0004309	7	8	6	5.2	97.3

• Explore on Target Illumination GWAS Analytics (TIGA)

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
sex hormone-binding globulin measurement	EFO_0004696	8		99.8
triglyceride measurement	EFO_0004530	17	3.1	99.1
self reported educational attainment	EFO_0004784	3	6.6	98.5
mean platelet volume	EFO_0004584	10		98.4
platelet count	EFO_0004309	6	5.2	97.3

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Orthologs (12)

1 – 5 of 12

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	jumonji domain containing 1C	VGNC:4718	450489
Macaque	jumonji domain containing 1C		697630
Mouse	jumonji domain containing 1C	MGI:1918614	108829
Rat	jumonji domain containing 1C	RGD:708458	171120
Dog	jumonji domain containing 1C	VGNC:42187	479221

Species	Name	OMA	EggNOG	Inparanoid
Chimp	jumonji domain containing 1C
Macaque	jumonji domain containing 1C
Mouse	jumonji domain containing 1C
Rat	jumonji domain containing 1C
Dog	jumonji domain containing 1C

Protein Structure (2 Structures, 1 AlphaFold Model)

Representation

  axes   backbone   ball+stick   cartoon   rocket   rope   spacefill

Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-Q15652-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 2 of 2

PDB Structure Id	Ligand	Method	Resolution (Å)	Residues	Fraction of Total Protein	Pub Year	Title

PDB Structure Id	Fraction of Total Protein	Resolution	Pub Year

Pathways (4)

Reactome (2)

KEGG (1)

WikiPathways (1)

Factors involved in megakaryocyte development and platelet production (R-HSA-983231)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Factors involved in megakaryocyte development and platelet production	139 targets	R-HSA-983231
Reactome	Hemostasis	666 targets	R-HSA-109582

Name	Explore in Pharos	Explore in Source
Factors involved in megakaryocyte development and platelet production	139 targets	R-HSA-983231
Hemostasis	666 targets	R-HSA-109582

Gene Ontology Terms (13)

Functions (6)

Components (4)

Processes (3)

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Items per page:

10

1 – 6 of 6

GO Term	Evidence	Assigned by
chromatin DNA binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
histone demethylase activity (H3-K9 specific)	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
transcription regulatory region sequence-specific DNA binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
thyroid hormone receptor binding	Traceable Author Statement (TAS)	UniProtKB
dioxygenase activity	Inferred from Electronic Annotation (IEA)	UniProtKB-KW
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

Protein-Protein Interactions (58)

Explore Interacting Targets

1 – 10 of 58

• See Interactions on String-DB

KDM4B

Tchem

Family: Epigenetic

Novelty: 0.01615072

Score: 0.911

Data Source: STRINGDB

KDM4C

Tchem

Family: Epigenetic

Novelty: 0.01347559

Score: 0.818

Data Source: STRINGDB

KDM4A

Tchem

Family: Epigenetic

Novelty: 0.00643043

Score: 0.818

Data Source: STRINGDB

NIPBL

Tbio

Novelty: 0.00462654

Score: 0.78

Data Source: STRINGDB

TP53BP1

Tbio

Family: Epigenetic

Novelty: 0.00131256

Score: 0.739

Data Source: STRINGDB

REEP3

Tbio

Novelty: 0.19673119

Score: 0.733

Data Source: STRINGDB

MDC1

Tbio

Novelty: 0.00533097

Score: 0.673

Data Source: STRINGDB

RD3

Tbio

Novelty: 0.00651981

Score: 0.664

Data Source: STRINGDB

RNF145

Tbio

Novelty: 0.30480192

Score: 0.651

Data Source: STRINGDB

BRPF1

Tchem

Family: Epigenetic

Novelty: 0.02524021

Score: 0.646

Data Source: STRINGDB

Publication Statistics

PubMed Score  37.84

PubMed score by year

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PubTator Score  23.31

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

3D-structure
Alternative splicing
Chromatin regulator
Complete proteome
Dioxygenase
Iron
Isopeptide bond
Metal-binding
Nucleus
Oxidoreductase

GWAS Trait Find Similar Targets

alcohol abuse
alkaline phosphatase measurement
apolipoprotein A 1 measurement
asthma
basophil percentage of granulocytes
basophil percentage of leukocytes
bilirubin measurement
BMI-adjusted waist-hip ratio
body height
chemokine (C-X-C motif) ligand 1 measurement

MGI Phenotype Find Similar Targets

cellular phenotype
endocrine/exocrine gland phenotype
mortality/aging
reproductive system phenotype
skeleton phenotype
vision/eye phenotype