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Aliases for PRDM5 Gene

Aliases for PRDM5 Gene

  • PR Domain 5 2 3
  • PR Domain Containing 5 2 3 5
  • PFM2 3 4
  • PR Domain-Containing Protein 5 4
  • EC 2.1.1.- 4
  • BCS2 3

External Ids for PRDM5 Gene

Previous GeneCards Identifiers for PRDM5 Gene

  • GC04M122540
  • GC04M121895
  • GC04M122009
  • GC04M122074
  • GC04M121973
  • GC04M121613
  • GC04M117343

Summaries for PRDM5 Gene

Entrez Gene Summary for PRDM5 Gene

  • The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]

GeneCards Summary for PRDM5 Gene

PRDM5 (PR Domain 5) is a Protein Coding gene. Diseases associated with PRDM5 include brittle cornea syndrome 2 and ehlers-danlos syndrome, type vi. GO annotations related to this gene include sequence-specific DNA binding and transcription regulatory region DNA binding.

UniProtKB/Swiss-Prot for PRDM5 Gene

  • Sequence-specific DNA-binding transcription factor. Represses transcription at least in part by recruitment of the histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1. Regulates hematopoiesis-associated protein-coding and microRNA (miRNA) genes. May regulate the expression of proteins involved in extracellular matrix development and maintenance, including fibrillar collagens, such as COL4A1 and COL11A1, connective tissue components, such as HAPLN1, and molecules regulating cell migration and adhesion, including EDIL3 and TGFB2. May caused G2/M arrest and apoptosis in cancer cells.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM5 Gene

Genomics for PRDM5 Gene

Regulatory Elements for PRDM5 Gene

Promoters for PRDM5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PRDM5 on UCSC Golden Path with GeneCards custom track

Genomic Location for PRDM5 Gene

Chromosome:
4
Start:
120,684,919 bp from pter
End:
120,922,870 bp from pter
Size:
237,952 bases
Orientation:
Minus strand

Genomic View for PRDM5 Gene

Genes around PRDM5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM5 Gene

Proteins for PRDM5 Gene

  • Protein details for PRDM5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQX1-PRDM5_HUMAN
    Recommended name:
    PR domain zinc finger protein 5
    Protein Accession:
    Q9NQX1
    Secondary Accessions:
    • Q0VAI9
    • Q0VAJ0
    • Q6NXQ7

    Protein attributes for PRDM5 Gene

    Size:
    630 amino acids
    Molecular mass:
    73090 Da
    Quaternary structure:
    • Interacts with EHMT2/G9A, GFI1 and HDAC1.

    Alternative splice isoforms for PRDM5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM5 Gene

Proteomics data for PRDM5 Gene at MOPED

Post-translational modifications for PRDM5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM5 Gene

No data available for DME Specific Peptides for PRDM5 Gene

Domains & Families for PRDM5 Gene

Gene Families for PRDM5 Gene

Protein Domains for PRDM5 Gene

Suggested Antigen Peptide Sequences for PRDM5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NQX1

UniProtKB/Swiss-Prot:

PRDM5_HUMAN :
  • Contains 1 SET domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 16 C2H2-type zinc fingers.
Domain:
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 16 C2H2-type zinc fingers.
genes like me logo Genes that share domains with PRDM5: view

Function for PRDM5 Gene

Molecular function for PRDM5 Gene

UniProtKB/Swiss-Prot Function:
Sequence-specific DNA-binding transcription factor. Represses transcription at least in part by recruitment of the histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1. Regulates hematopoiesis-associated protein-coding and microRNA (miRNA) genes. May regulate the expression of proteins involved in extracellular matrix development and maintenance, including fibrillar collagens, such as COL4A1 and COL11A1, connective tissue components, such as HAPLN1, and molecules regulating cell migration and adhesion, including EDIL3 and TGFB2. May caused G2/M arrest and apoptosis in cancer cells.

Enzyme Numbers (IUBMB) for PRDM5 Gene

Gene Ontology (GO) - Molecular Function for PRDM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 17636019
GO:0003676 nucleic acid binding IEA --
GO:0008168 methyltransferase activity IEA --
GO:0044212 transcription regulatory region DNA binding IDA 17636019
GO:0070491 repressing transcription factor binding IDA 17636019
genes like me logo Genes that share ontologies with PRDM5: view
genes like me logo Genes that share phenotypes with PRDM5: view

Human Phenotype Ontology for PRDM5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for PRDM5 Gene

miRTarBase miRNAs that target PRDM5

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PRDM5 Gene

Localization for PRDM5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM5 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PRDM5 Gene COMPARTMENTS Subcellular localization image for PRDM5 gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for PRDM5 Gene

Pathways & Interactions for PRDM5 Gene

SuperPathways for PRDM5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PRDM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IMP 17636019
GO:0051567 histone H3-K9 methylation IDA 17636019
genes like me logo Genes that share ontologies with PRDM5: view

No data available for Pathways by source and SIGNOR curated interactions for PRDM5 Gene

Drugs & Compounds for PRDM5 Gene

No Compound Related Data Available

Transcripts for PRDM5 Gene

Unigene Clusters for PRDM5 Gene

PR domain containing 5:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM5 Gene

No ASD Table

Relevant External Links for PRDM5 Gene

GeneLoc Exon Structure for
PRDM5
ECgene alternative splicing isoforms for
PRDM5

Expression for PRDM5 Gene

mRNA expression in normal human tissues for PRDM5 Gene

Protein differential expression in normal tissues from HIPED for PRDM5 Gene

This gene is overexpressed in Vitreous humor (43.3), Kidney (10.7), Placenta (7.1), and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PRDM5 Gene



SOURCE GeneReport for Unigene cluster for PRDM5 Gene Hs.666782

mRNA Expression by UniProt/SwissProt for PRDM5 Gene

Q9NQX1-PRDM5_HUMAN
Tissue specificity: Widely expressed with highest levels in colon and ovary. Tends to be silenced in breast, colorectal, gastric and liver cancer tissues.
genes like me logo Genes that share expression patterns with PRDM5: view

Protein tissue co-expression partners for PRDM5 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PRDM5 Gene

Orthologs for PRDM5 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM5 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PRDM5 35
  • 92.59 (n)
  • 96.03 (a)
PRDM5 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PRDM5 35
  • 89.14 (n)
  • 90.73 (a)
PRDM5 36
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm5 35
  • 87.7 (n)
  • 92.49 (a)
Prdm5 16
Prdm5 36
  • 93 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PRDM5 35
  • 99.63 (n)
  • 99.84 (a)
PRDM5 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Prdm5 35
  • 87.48 (n)
  • 92.32 (a)
oppossum
(Monodelphis domestica)
Mammalia PRDM5 36
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 87 (a)
OneToMany
-- 36
  • 80 (a)
OneToMany
chicken
(Gallus gallus)
Aves PRDM5 35
  • 81.69 (n)
  • 85.71 (a)
PRDM5 36
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM5 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm5 35
  • 77.25 (n)
  • 82.38 (a)
zebrafish
(Danio rerio)
Actinopterygii prdm5 35
  • 70.07 (n)
  • 78.59 (a)
prdm5 36
  • 78 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG10669 37
  • 26 (a)
CG11695 37
  • 26 (a)
CG11696 37
  • 30 (a)
CG8388 37
  • 27 (a)
su(Hw) 37
  • 33 (a)
CG11456 36
  • 24 (a)
OneToMany
CG1233 36
  • 13 (a)
OneToMany
Species with no ortholog for PRDM5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PRDM5 Gene

ENSEMBL:
Gene Tree for PRDM5 (if available)
TreeFam:
Gene Tree for PRDM5 (if available)

Paralogs for PRDM5 Gene

(358) SIMAP similar genes for PRDM5 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with PRDM5: view

No data available for Paralogs for PRDM5 Gene

Variants for PRDM5 Gene

Sequence variations from dbSNP and Humsavar for PRDM5 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
VAR_066393 Brittle cornea syndrome 2 (BCS2)
rs2290 -- 120,734,912(-) GAAGA(A/C)AACGA intron-variant
rs237212 -- 120,817,027(-) AAAAG(A/G)GATCA intron-variant
rs343166 -- 120,897,567(-) GAGGA(G/T)GTAGA intron-variant
rs343167 -- 120,897,351(-) AAACA(A/G)TAAGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PRDM5 Gene

Variant ID Type Subtype PubMed ID
nsv879852 CNV Gain 21882294
nsv461634 CNV Gain 19166990
nsv507192 CNV Insertion 20534489
dgv5701n71 CNV Loss 21882294
esv2472537 CNV Deletion 19546169
esv2728246 CNV Deletion 23290073
nsv4490 CNV Loss 18451855
esv1970766 CNV Deletion 18987734
esv2728247 CNV Deletion 23290073
nsv292623 CNV Loss 16902084
nsv4491 CNV Insertion 18451855
esv2728248 CNV Deletion 23290073

Variation tolerance for PRDM5 Gene

Residual Variation Intolerance Score: 12.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.25; 52.69% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PRDM5 Gene

HapMap Linkage Disequilibrium report
PRDM5
Human Gene Mutation Database (HGMD)
PRDM5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM5 Gene

Disorders for PRDM5 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PRDM5 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
brittle cornea syndrome 2
  • bcs2
ehlers-danlos syndrome, type vi
  • type vi ehlers-danlos syndrome
irregular astigmatism
keratoconus
  • conical cornea
axenfeld-rieger syndrome, type 3
  • anterior segment mesenchymal dysgenesis
- elite association - COSMIC cancer census association via MalaCards
Search PRDM5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PRDM5_HUMAN
  • Brittle cornea syndrome 2 (BCS2) [MIM:614170]: A disorder characterized by extreme corneal thinning resulting in corneal rupture after minor trauma, blue sclerae, keratoconus or keratoglobus, hyperelasticity of the skin, and hypermobile joints. {ECO:0000269 PubMed:21664999}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PRDM5

Genetic Association Database (GAD)
PRDM5
Human Genome Epidemiology (HuGE) Navigator
PRDM5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRDM5
genes like me logo Genes that share disorders with PRDM5: view

No data available for Genatlas for PRDM5 Gene

Publications for PRDM5 Gene

  1. PRDM5 is silenced in human cancers and has growth suppressive activities. (PMID: 15077163) Deng Q. … Huang S. (Oncogene 2004) 3 4 23 67
  2. Prdm5 suppresses Apc(Min)-driven intestinal adenomas and regulates monoacylglycerol lipase expression. (PMID: 23873026) Galli G.G. … Lund A.H. (Oncogene 2014) 3
  3. Promoter methylation-mediated downregulation of PRDM5 contributes to the development of lung squamous cell carcinoma. (PMID: 24395656) Tan S.X. … Liu W.E. (Tumour Biol. 2014) 3
  4. Methylation of PRDM2, PRDM5 and PRDM16 genes in lung cancer cells. (PMID: 24966940) Tan S.X. … Liu W.E. (Int J Clin Exp Pathol 2014) 3
  5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PMID: 23251661) Comuzzie A.G. … Butte N.F. (PLoS ONE 2012) 3

Products for PRDM5 Gene

Sources for PRDM5 Gene

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