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Aliases for PRDM5 Gene

Aliases for PRDM5 Gene

  • PR Domain Containing 5 2 3
  • PFM2 3 4
  • BCS2 3 6
  • PR Domain Zinc Finger Protein 5 3
  • PR Domain-Containing Protein 5 4
  • EC 2.1.1.- 4

External Ids for PRDM5 Gene

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 Containing 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 methyltransferase activity.

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

Genomic Location for PRDM5 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PRDM5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM5 Gene

Regulatory Elements 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 for PRDM5 Gene

Gene Families for PRDM5 Gene

HGNC:
  • ZNF :Zinc fingers, C2H2-type

Protein Domains for PRDM5 Gene

UniProtKB/Swiss-Prot:

PRDM5_HUMAN
Domain:
  • Contains 1 SET domain.:
    • Q9NQX1
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.:
    • Q9NQX1
Similarity:
  • Contains 16 C2H2-type zinc fingers.:
    • Q9NQX1
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:0000976 transcription regulatory region sequence-specific DNA binding --
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 17636019
GO:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription IDA 17636019
GO:0005515 protein binding IPI 17636019
GO:0008168 methyltransferase activity IEA --
genes like me logo Genes that share ontologies with PRDM5: view

Phenotypes for PRDM5 Gene

MGI mutant phenotypes for PRDM5:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with PRDM5: view

No data available for Animal Models , miRNA , Transcription Factor Targeting 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
extracellular 1

Gene Ontology (GO) - Cellular Components for PRDM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 17636019
genes like me logo Genes that share ontologies with PRDM5: view

Pathways 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:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 17636019
GO:0000278 mitotic cell cycle IMP 17636019
GO:0006351 transcription, DNA-templated IEA --
GO:0016575 histone deacetylation IMP 17636019
GO:0045892 negative regulation of transcription, DNA-templated IDA 17636019
genes like me logo Genes that share ontologies with PRDM5: view

No data available for Pathways by source for PRDM5 Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with PRDM5: view

Orthologs for PRDM5 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM5 36
  • 99.63 (n)
  • 99.84 (a)
PRDM5 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PRDM5 36
  • 92.59 (n)
  • 96.03 (a)
PRDM5 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PRDM5 36
  • 89.14 (n)
  • 90.73 (a)
PRDM5 37
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prdm5 36
  • 87.7 (n)
  • 92.49 (a)
Prdm5 16
Prdm5 37
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRDM5 37
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 87 (a)
OneToMany
-- 37
  • 80 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Prdm5 36
  • 87.48 (n)
  • 92.32 (a)
chicken
(Gallus gallus)
Aves PRDM5 36
  • 81.69 (n)
  • 85.71 (a)
PRDM5 37
  • 81 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PRDM5 37
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia prdm5 36
  • 77.25 (n)
  • 82.38 (a)
zebrafish
(Danio rerio)
Actinopterygii prdm5 36
  • 70.07 (n)
  • 78.59 (a)
prdm5 37
  • 78 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG11456 37
  • 24 (a)
OneToMany
CG1233 37
  • 13 (a)
OneToMany
su(Hw) 38
  • 33 (a)
CG10669 38
  • 26 (a)
CG11695 38
  • 26 (a)
CG11696 38
  • 30 (a)
CG8388 38
  • 27 (a)
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

Selected 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 MAF
rs2290 -- 120,734,912(-) GAAGA(A/C)AACGA intron-variant
rs168224 -- 120,893,863(-) aaaga(C/G)aaatg intron-variant
rs168225 -- 120,890,021(-) cttaa(A/G)gatgc intron-variant
rs168226 -- 120,821,615(-) TAAGG(C/T)CAGTT intron-variant
rs171067 -- 120,838,534(+) tggca(C/T)cagga 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

Relevant External Links for PRDM5 Gene

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

Disorders for PRDM5 Gene

(1) OMIM Diseases for PRDM5 Gene (614161)

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.

(1) University of Copenhagen DISEASES for PRDM5 Gene

Relevant External Links for PRDM5

Genetic Association Database (GAD)
PRDM5
Human Genome Epidemiology (HuGE) Navigator
PRDM5
genes like me logo Genes that share disorders with PRDM5: view

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
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. Epigenetic regulation of protein-coding and microRNA genes by the Gfi1-interacting tumor suppressor PRDM5. (PMID: 17636019) Duan Z. … Horwitz M.S. (Mol. Cell. Biol. 2007) 3 4
  4. PRDM5 identified as a target of epigenetic silencing in colorectal and gastric cancer. (PMID: 17699856) Watanabe Y. … Tokino T. (Clin. Cancer Res. 2007) 3 4
  5. Genome-wide association with diabetes-related traits in the Framingham Heart Study. (PMID: 17903298) Meigs J.B. … Dupuis J. (BMC Med. Genet. 2007) 3 49

Products for PRDM5 Gene

Sources for PRDM5 Gene

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