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PPEF1 Gene(Protein Coding)

Protein Phosphatase With EF-Hand Domain 1

GCID:
GC0XP018694
GIFtS:
43
Genes Participants
UDN Logo

Aliases for PPEF1 Gene

Aliases for PPEF1 Gene

  • Protein Phosphatase With EF-Hand Domain 1 2 3 5
  • Protein Phosphatase 7, Catalytic Subunit, Alpha Isozyme 2 3
  • Protein Phosphatase, EF-Hand Calcium Binding Domain 1 2 3
  • Protein Phosphatase With EF Calcium-Binding Domain 3 4
  • PPP7C 3 4
  • PPEF 3 4
  • PP7 3 4
  • Protein Phosphatase, Serine/Threonine Type, With EF-Hands 3
  • Serine/Threonine-Protein Phosphatase With EF-Hands 1 3
  • Serine/Threonine Protein Phosphatase 7 3
  • Serine/Threonine-Protein Phosphatase 7 4
  • EC 3.1.3.16 4
  • PPP7CA 3
  • PPEF-1 4

External Ids for PPEF1 Gene

Previous HGNC Symbols for PPEF1 Gene

  • PPEF

Previous GeneCards Identifiers for PPEF1 Gene

  • GC0XP018253
  • GC0XP017375
  • GC0XP017911
  • GC0XP018070
  • GC0XP018468
  • GC0XP018618
  • GC0XP016462

Summaries for PPEF1 Gene

Entrez Gene Summary for PPEF1 Gene

  • This gene encodes a member of the serine/threonine protein phosphatase with EF-hand motif family. The protein contains a protein phosphatase catalytic domain, and at least two EF-hand calcium-binding motifs in its C terminus. Although its substrate(s) is unknown, the encoded protein has been suggested to play a role in specific sensory neuron function and/or development. This gene shares high sequence similarity with the Drosophila retinal degeneration C (rdgC) gene. Several alternatively spliced transcript variants, each encoding a distinct isoform, have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for PPEF1 Gene

PPEF1 (Protein Phosphatase With EF-Hand Domain 1) is a Protein Coding gene. Diseases associated with PPEF1 include Retinal Degeneration and Juvenile Retinoschisis. Among its related pathways are Phototransduction and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include calcium ion binding and iron ion binding. An important paralog of this gene is PPEF2.

UniProtKB/Swiss-Prot for PPEF1 Gene

  • May have a role in the recovery or adaptation response of photoreceptors. May have a role in development.

Gene Wiki entry for PPEF1 Gene

Additional gene information for PPEF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PPEF1 Gene

Genomics for PPEF1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PPEF1 Gene

Promoters and enhancers for PPEF1 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
GH0XJ018674 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE 650.7 -0.9 -863 1.7 ATF1 SIN3A BRCA1 NCOA2 YY1 GTF3C2 GLIS2 ZNF213 ELK1 ZNF207 PPEF1 TRV-TAC1-2 CDKL5 PHKA2
GH0XJ018707 Promoter 0.8 EPDnew 650.3 +31.7 31729 0.1 OSR2 POLR2A L3MBTL2 PRDM10 PRDM4 TRIM28 PPEF1 PIR41454 GC0XM018732 GC0XM018733 GC0XM018735 PIR45897
GH0XJ018690 Promoter 0.5 EPDnew 650.4 +15.0 15035 0.1 PPEF1-AS1 PPEF1
GH0XJ018701 Enhancer 0.9 ENCODE 0.3 +26.3 26260 1.8 NFIB ZSCAN4 KLF17 MZF1 SIN3A FEZF1 RAD21 BRCA1 ZNF121 ZNF213 PIR41454 GC0XM018732 GC0XM018733 GC0XM018735 PIR45897 PPEF1
GH0XJ018698 Enhancer 0.4 ENCODE 0.3 +23.0 22988 0.2 CEBPB FEZF1 PIR41454 PPEF1-AS1 PPEF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PPEF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PPEF1 gene promoter:
  • deltaCREB
  • CREB
  • PPAR-gamma2
  • PPAR-gamma1
  • GCNF-2
  • GCNF-1
  • GCNF
  • RORalpha1

Genomic Locations for PPEF1 Gene

Genomic Locations for PPEF1 Gene
chrX:18,675,909-18,827,921
(GRCh38/hg38)
Size:
152,013 bases
Orientation:
Plus strand
chrX:18,694,029-18,846,039
(GRCh37/hg19)
Size:
152,011 bases
Orientation:
Plus strand

Genomic View for PPEF1 Gene

Genes around PPEF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PPEF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PPEF1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PPEF1 Gene

Proteins for PPEF1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PPEF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14829-PPE1_HUMAN
    Recommended name:
    Serine/threonine-protein phosphatase with EF-hands 1
    Protein Accession:
    O14829
    Secondary Accessions:
    • A6NHP4
    • A8K348
    • O15253
    • Q9NU21
    • Q9UJH0

    Protein attributes for PPEF1 Gene

    Size:
    653 amino acids
    Molecular mass:
    75792 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PPEF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PPEF1 Gene

Protein Expression for PPEF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PPEF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PPEF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PPEF1 Gene

Domains & Families for PPEF1 Gene

Gene Families for PPEF1 Gene

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

Protein Domains for PPEF1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PPEF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O14829

UniProtKB/Swiss-Prot:

PPE1_HUMAN :
  • Belongs to the PPP phosphatase family.
Family:
  • Belongs to the PPP phosphatase family.
genes like me logo Genes that share domains with PPEF1: view

Function for PPEF1 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PPEF1 Gene

UniProtKB/Swiss-Prot Function:
May have a role in the recovery or adaptation response of photoreceptors. May have a role in development.
UniProtKB/Swiss-Prot CatalyticActivity:
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by calcium.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
pH dependence: Optimum pH is 8.0.;
GENATLAS Biochemistry:
serine-threonine phosphatase with two alternatively spliced forms,expressed in sensory neurons of neural crest origin,homologous to Drosophila retinal degeneration C (rdgc)

Enzyme Numbers (IUBMB) for PPEF1 Gene

Gene Ontology (GO) - Molecular Function for PPEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004722 protein serine/threonine phosphatase activity TAS --
GO:0005506 iron ion binding IEA --
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PPEF1: view
genes like me logo Genes that share phenotypes with PPEF1: view

Animal Models for PPEF1 Gene

MGI Knock Outs for PPEF1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PPEF1

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PPEF1 Gene

Localization for PPEF1 Gene

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 PPEF1 gene
Compartment Confidence
cytosol 5
mitochondrion 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PPEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PPEF1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PPEF1 Gene

Pathways & Interactions for PPEF1 Gene

genes like me logo Genes that share pathways with PPEF1: view

Gene Ontology (GO) - Biological Process for PPEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation TAS 9215685
GO:0022400 regulation of rhodopsin mediated signaling pathway TAS --
GO:0050906 detection of stimulus involved in sensory perception IEA --
genes like me logo Genes that share ontologies with PPEF1: view

No data available for SIGNOR curated interactions for PPEF1 Gene

Drugs & Compounds for PPEF1 Gene

Products:

  1. Drug

(7) Drugs for PPEF1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
calcium Approved Nutra 0
Magnesium Approved Nutra 0
Manganese Approved Nutra 37

(2) Additional Compounds for PPEF1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Fe2+
  • FE (II) ion
  • Fe(II)
  • Fe(2+)
  • Ferrous ion
  • Iron ion(2+)
 15438-31-0
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
 14265-44-2
genes like me logo Genes that share compounds with PPEF1: view

Transcripts for PPEF1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PPEF1 Gene

(6) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(38) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PPEF1 Gene

Protein phosphatase, EF-hand calcium binding domain 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PPEF1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PPEF1 Gene

No ASD Table

Relevant External Links for PPEF1 Gene

GeneLoc Exon Structure for
PPEF1
ECgene alternative splicing isoforms for
PPEF1

Expression for PPEF1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PPEF1 Gene

mRNA expression in normal human tissues for PPEF1 Gene
mRNA expression by GTEx for PPEF1 GenemRNA expression by BioGPS for PPEF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PPEF1 Gene

This gene is overexpressed in Testis (x14.4), Brain - Spinal cord (cervical c-1) (x7.6), Brain - Anterior cingulate cortex (BA24) (x5.8), Brain - Cortex (x4.8), and Brain - Frontal Cortex (BA9) (x4.5).

Protein differential expression in normal tissues from HIPED for PPEF1 Gene

This gene is overexpressed in Spinal cord (60.4) and Testis (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PPEF1 Gene



Protein tissue co-expression partners for PPEF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PPEF1 Gene:

PPEF1

SOURCE GeneReport for Unigene cluster for PPEF1 Gene:

Hs.211589

mRNA Expression by UniProt/SwissProt for PPEF1 Gene:

O14829-PPE1_HUMAN
Tissue specificity: Detected in retina and retinal derived Y-79 retinoblastoma cells. Also found in fetal brain.

Evidence on tissue expression from TISSUES for PPEF1 Gene

  • Nervous system(4.6)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with PPEF1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PPEF1 Gene

Orthologs for PPEF1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PPEF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PPEF1 34 33
  • 93.73 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia PPEF1 34 33
  • 85.94 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia PPEF1 34 33
  • 83.59 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Ppef1 33
  • 81.45 (n)
mouse
(Mus musculus)
 Mammalia Ppef1 16 34 33
  • 80.52 (n)
oppossum
(Monodelphis domestica)
 Mammalia PPEF1 34
  • 57 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PPEF1 34
  • 43 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PPEF1 34 33
  • 62.74 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia PPEF1 34
  • 52 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia ppef1 33
  • 62.14 (n)
zebrafish
(Danio rerio)
 Actinopterygii ppef1 34 33
  • 58.83 (n)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta rdgC 34 35
  • 36 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea pef-1 34 33
  • 52.57 (n)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes PPT1 34
  • 20 (a)
 OneToMany
Species where no ortholog for PPEF1 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)
  • 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)

Evolution for PPEF1 Gene

ENSEMBL:
Gene Tree for PPEF1 (if available)
TreeFam:
Gene Tree for PPEF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PPEF1: view image

Paralogs for PPEF1 Gene

Paralogs for PPEF1 Gene

(4) SIMAP similar genes for PPEF1 Gene using alignment to 6 proteins:

  • PPE1_HUMAN
  • B7Z6R7_HUMAN
  • C9JY08_HUMAN
  • F8W7X9_HUMAN
  • F8WC69_HUMAN
  • H7C592_HUMAN
genes like me logo Genes that share paralogs with PPEF1: view

Variants for PPEF1 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PPEF1 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000015083 -- 18,819,184(+) A/T intron_variant
rs1000017683 -- 18,688,292(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000032113 -- 18,677,638(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000065896 -- 18,794,767(+) T/A intron_variant
rs1000086467 -- 18,713,589(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PPEF1 Gene

Variant ID Type Subtype PubMed ID
esv2752317 CNV gain 17911159
esv33517 CNV loss 17666407
esv3576793 CNV gain 25503493

Variation tolerance for PPEF1 Gene

Residual Variation Intolerance Score: 21.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.81; 34.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PPEF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PPEF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PPEF1 Gene

Disorders for PPEF1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PPEF1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
retinal degeneration
  • degeneration of retina
juvenile retinoschisis
  • x-linked juvenile retinoschisis
pineal parenchymal tumor of intermediate differentiation
  • pineal parenchymal tumour of intermediate differentiation
- elite association - COSMIC cancer census association via MalaCards
Search PPEF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PPEF1

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PPEF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PPEF1 Gene

Publications for PPEF1 Gene

  1. A novel human serine-threonine phosphatase related to the Drosophila retinal degeneration C (rdgC) gene is selectively expressed in sensory neurons of neural crest origin. (PMID: 9215685) Montini E … Franco B (Human molecular genetics 1997) 2 3 4 22 58
  2. Identification and characterization of a conserved family of protein serine/threonine phosphatases homologous to Drosophila retinal degeneration C. (PMID: 9326663) Sherman PM … Nathans J (Proceedings of the National Academy of Sciences of the United States of America 1997) 2 3 4 58
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  4. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

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