This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013] See more...

Aliases for PRDM7 Gene

Aliases for PRDM7 Gene

  • PR/SET Domain 7 2 3 5
  • Probable Histone-Lysine N-Methyltransferase PRDM7 3 4
  • PR Domain Zinc Finger Protein 7 3 4
  • PR Domain Containing 7 2 3
  • PR Domain 7 2 3
  • PFM4 3 4
  • PR Domain-Containing Protein 7 4
  • PR-Domain Family Protein 4 3
  • EC 2.1.1.43 52
  • EC 2.1.1.- 4
  • ZNF910 3

External Ids for PRDM7 Gene

Previous GeneCards Identifiers for PRDM7 Gene

  • GC16M081443
  • GC16M091111
  • GC16M089824
  • GC16M089865
  • GC16M088650
  • GC16M090122
  • GC16M075814

Summaries for PRDM7 Gene

Entrez Gene Summary for PRDM7 Gene

  • This gene encodes a member of a family of proteins that may have roles in transcription and other nuclear processes. The encoded protein contains a KRAB (Kruppel-associated box) domain -A box and a SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain and may function as a histone methyltransferase. [provided by RefSeq, Aug 2013]

GeneCards Summary for PRDM7 Gene

PRDM7 (PR/SET Domain 7) is a Protein Coding gene. Among its related pathways are Gene Expression and Metabolism. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and histone-lysine N-methyltransferase activity. An important paralog of this gene is PRDM11.

UniProtKB/Swiss-Prot Summary for PRDM7 Gene

Additional gene information for PRDM7 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM7 Gene

Genomics for PRDM7 Gene

GeneHancer (GH) Regulatory Elements for PRDM7 Gene

Promoters and enhancers for PRDM7 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J090076 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 500.4 +14.2 14225 1.9 CTCF NRF1 SP1 ZIC2 CLOCK FOS NFYB ZNF341 RBM25 OSR2 PRDM7 CDK10 ACSF3 ENSG00000261118 TCF25 ENSG00000261172 AFG3L1P ENSG00000268218 ZNF276 MC1R
GH16J090093 Enhancer 0.3 Ensembl 500.7 -1.1 -1129 0.4 FOS TUBB8P7 PRDM7 lnc-PRDM7-3 piR-37193-002
GH16J090018 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 16.4 +71.2 71171 6.2 ZBTB40 ZNF217 CTCF TCF12 NRF1 POLR2G NCOR1 GTF2E2 PHF8 FOS DBNDD1 GAS8 DEF8 PRDM7 SNORD68 ACSF3 RPL13 URAHP AFG3L1P ENSG00000261118
GH16J089853 Enhancer 0.6 FANTOM5 dbSUPER 3.4 +238.6 238570 0.1 RXRA HNF4A SP1 LOC105371419 GAS8-AS1 DBNDD1 PRDM7 DPEP1 RF00017-2194 SPIRE2
GH16J090081 Promoter/Enhancer 1.4 ENCODE CraniofacialAtlas 0.4 +9.9 9852 1.3 ZNF217 CTCF TCF12 MYC NRF1 PHF8 ZFX ZNF639 CLOCK ZBTB11 lnc-GAS8-6 DEF8 CDK10 ENSG00000261172 TUBB8P7 FAM157C FANCA PRDM7 lnc-PRDM7-3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM7 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM7

Top Transcription factor binding sites by QIAGEN in the PRDM7 gene promoter:
  • E47
  • LCR-F1
  • p53
  • RFX1
  • SRF
  • SRF (504 AA)
  • Tal-1
  • ZID

Genomic Locations for PRDM7 Gene

Genomic Locations for PRDM7 Gene
chr16:90,056,566-90,092,072
(GRCh38/hg38)
Size:
35,507 bases
Orientation:
Minus strand
chr16:90,122,974-90,158,480
(GRCh37/hg19)
Size:
35,507 bases
Orientation:
Minus strand

Genomic View for PRDM7 Gene

Genes around PRDM7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRDM7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM7 Gene

Proteins for PRDM7 Gene

  • Protein details for PRDM7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQW5-PRDM7_HUMAN
    Recommended name:
    Probable histone-lysine N-methyltransferase PRDM7
    Protein Accession:
    Q9NQW5
    Secondary Accessions:
    • A4Q9G8
    • Q08EM4
    • Q9NQW4

    Protein attributes for PRDM7 Gene

    Size:
    492 amino acids
    Molecular mass:
    55777 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • The mouse orthologous protein seems not to exist. According to PubMed:17916234, human PRDM7 and PRDM9 genes, a pair of close paralogs corresponding to a single mouse gene Prdm9, were generated by a recent gene duplication event after the divergence of the ancestors of human and mouse.
    • [Isoform 3]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for PRDM7 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PRDM7 Gene

Selected DME Specific Peptides for PRDM7 Gene

Q9NQW5:
  • EQNLVAFQ
  • GDEYGQELGI

Post-translational modifications for PRDM7 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for PRDM7 Gene

Gene Families for PRDM7 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for PRDM7 Gene

Blocks:
  • C2H2-type zinc finger signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PRDM7 Gene

GenScript: Design optimal peptide antigens:
  • PR domain-containing protein 7 (PRDM7_HUMAN)
genes like me logo Genes that share domains with PRDM7: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PRDM7 Gene

Function for PRDM7 Gene

Molecular function for PRDM7 Gene

UniProtKB/Swiss-Prot Function:
Probable histone methyltransferase.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929;.

Enzyme Numbers (IUBMB) for PRDM7 Gene

Phenotypes From GWAS Catalog for PRDM7 Gene

Gene Ontology (GO) - Molecular Function for PRDM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0003676 nucleic acid binding IEA --
GO:0003700 DNA-binding transcription factor activity IBA 21873635
GO:0005515 protein binding IPI,IEA 25416956
genes like me logo Genes that share ontologies with PRDM7: view
genes like me logo Genes that share phenotypes with PRDM7: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM7

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PRDM7 Gene

Localization for PRDM7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM7 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRDM7 gene
Compartment Confidence
nucleus 4
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRDM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IBA 21873635
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with PRDM7: view

Pathways & Interactions for PRDM7 Gene

PathCards logo

SuperPathways for PRDM7 Gene

genes like me logo Genes that share pathways with PRDM7: view

Pathways by source for PRDM7 Gene

2 Reactome pathways for PRDM7 Gene
2 KEGG pathways for PRDM7 Gene

Gene Ontology (GO) - Biological Process for PRDM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0010845 positive regulation of reciprocal meiotic recombination IBA 21873635
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with PRDM7: view

No data available for SIGNOR curated interactions for PRDM7 Gene

Drugs & Compounds for PRDM7 Gene

(1) Drugs for PRDM7 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for PRDM7 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with PRDM7: view

Transcripts for PRDM7 Gene

mRNA/cDNA for PRDM7 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM7

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM7 Gene

No ASD Table

Relevant External Links for PRDM7 Gene

GeneLoc Exon Structure for
PRDM7

Expression for PRDM7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRDM7 Gene

mRNA differential expression in normal tissues according to GTEx for PRDM7 Gene

This gene is overexpressed in Testis (x40.9).

Protein differential expression in normal tissues from HIPED for PRDM7 Gene

This gene is overexpressed in Frontal cortex (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PRDM7 Gene



Protein tissue co-expression partners for PRDM7 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM7

SOURCE GeneReport for Unigene cluster for PRDM7 Gene:

Hs.406695
genes like me logo Genes that share expression patterns with PRDM7: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRDM7 Gene

Orthologs for PRDM7 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM7 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PRDM7 31
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRDM7 31
  • 57 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PRDM7 31
  • 56 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRDM7 31
  • 1 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii PRDM7 31
  • 2 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG43347 31
  • 3 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-17 30
  • 46.25 (n)
Species where no ortholog for PRDM7 was found in the sources mined by GeneCards:
  • 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for PRDM7 Gene

ENSEMBL:
Gene Tree for PRDM7 (if available)
TreeFam:
Gene Tree for PRDM7 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM7: view image

Paralogs for PRDM7 Gene

Paralogs for PRDM7 Gene

(3) SIMAP similar genes for PRDM7 Gene using alignment to 2 proteins:

  • PRDM7_HUMAN
  • H3BUJ3_HUMAN

Pseudogenes.org Pseudogenes for PRDM7 Gene

genes like me logo Genes that share paralogs with PRDM7: view

Variants for PRDM7 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM7 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs12925933 - p.Asp90Glu
rs2078478 - p.Arg131Lys
rs7206111 - p.Asn435Lys

Additional dbSNP identifiers (rs#s) for PRDM7 Gene

Structural Variations from Database of Genomic Variants (DGV) for PRDM7 Gene

Variant ID Type Subtype PubMed ID
dgv3067n100 CNV gain 25217958
esv1938258 CNV deletion 18987734
esv2550224 CNV deletion 19546169
esv2660381 CNV deletion 23128226
esv28486 CNV loss 19812545
esv3553924 CNV deletion 23714750
esv3639606 CNV gain 21293372
esv3639607 CNV gain 21293372
esv3639609 CNV loss 21293372
esv3639610 CNV gain 21293372
esv3639611 CNV loss 21293372
esv3639612 CNV gain 21293372
nsv1059965 CNV gain 25217958
nsv1062080 CNV loss 25217958
nsv1064351 CNV gain+loss 25217958
nsv1067164 CNV gain+loss 25217958
nsv1934 CNV deletion 18451855
nsv428331 CNV gain+loss 18775914
nsv457626 CNV loss 19166990
nsv471119 CNV loss 18288195
nsv471120 CNV gain 18288195
nsv482951 CNV loss 15286789
nsv509641 CNV insertion 20534489
nsv514823 CNV gain 21397061
nsv573841 CNV loss 21841781
nsv9482 CNV loss 18304495
nsv978180 CNV duplication 23825009

Variation tolerance for PRDM7 Gene

Residual Variation Intolerance Score: 98.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.05; 95.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRDM7 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM7

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM7 Gene

Disorders for PRDM7 Gene

Additional Disease Information for PRDM7

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PRDM7 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRDM7 Gene

Publications for PRDM7 Gene

  1. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. (PMID: 17916234) Fumasoni I … Ciccarelli FD (BMC evolutionary biology 2007) 2 3 4 54
  2. PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase. (PMID: 27129774) Blazer LL … Vedadi M (The Journal of biological chemistry 2016) 2 3 54
  3. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 54
  4. The yin-yang of PR-domain family genes in tumorigenesis. (PMID: 10668202) Jiang GL … Huang S (Histology and histopathology 2000) 3 4 54
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 54

Products for PRDM7 Gene

Sources for PRDM7 Gene