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Aliases for PEF1 Gene

Aliases for PEF1 Gene

  • Penta-EF-Hand Domain Containing 1 2 3 5
  • PEF Protein With A Long N-Terminal Hydrophobic Domain 3 4
  • Peflin 2 3
  • ABP32 3 4
  • Penta-EF Hand Domain-Containing Protein 1 4
  • PEF1A 3

External Ids for PEF1 Gene

Previous GeneCards Identifiers for PEF1 Gene

  • GC01M031765
  • GC01U901184
  • GC01M031868
  • GC01M032095
  • GC01M030212

Summaries for PEF1 Gene

Entrez Gene Summary for PEF1 Gene

  • This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. The encoded protein has been shown to form a heterodimer with the programmed cell death 6 gene product and may modulate its function in Ca(2+) signaling. Alternative splicing results in multiple transcript variants and a pseudogene has been identified on chromosome 1.[provided by RefSeq, May 2010]

GeneCards Summary for PEF1 Gene

PEF1 (Penta-EF-Hand Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is PDCD6.

UniProtKB/Swiss-Prot for PEF1 Gene

  • Calcium-binding protein that acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium. Together with PDCD6, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in endoplasmic reticulum (ER)-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PDCD6 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Its role in the heterodimer formed with PDCD6 is however unclear: some evidences show that PEF1 and PDCD6 work together and promote association between PDCD6 and SEC31 in presence of calcium (PubMed:27716508). Other reports show that PEF1 dissociates from PDCD6 in presence of calcium, and may act as a negative regulator of PDCD6 (PubMed:11278427). Also acts as a negative regulator of ER-Golgi transport; possibly by inhibiting interaction between PDCD6 and SEC31 (By similarity).

Gene Wiki entry for PEF1 Gene

Additional gene information for PEF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PEF1 Gene

Genomics for PEF1 Gene

GeneHancer (GH) Regulatory Elements for PEF1 Gene

Promoters and enhancers for PEF1 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
GH01J031643 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 659.6 -3.0 -2971 10.2 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 PEF1 GC01M031634 SNRNP40 KPNA6 TXLNA TSSK3 EIF3I FAM229A COL16A1 LOC105378626
GH01J031787 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -143.7 -143709 2.9 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A FEZF1 ZNF2 YY1 POLR2B ENSG00000254545 SNRNP40 TSSK3 TMEM39B RBBP4 COL16A1 TXLNA ENSG00000229447 KHDRBS1 FAM229A
GH01J031668 Enhancer 1.2 Ensembl ENCODE dbSUPER 18.5 -26.9 -26943 7.6 NFIB SIN3A ZNF2 RAD21 ZNF335 GLIS2 ZNF366 SCRT2 RCOR1 YY2 SNRNP40 PEF1 TSSK3 TXLNA RBBP4 TMEM39B COL16A1 KHDRBS1 LOC105378626 TINAGL1
GH01J031699 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 10.6 -57.5 -57543 6.7 SMAD1 FOXA2 MLX ARID4B DMAP1 E2F8 ZNF143 FOS DEK SP5 COL16A1 ENSG00000235790 ADGRB2 SNRNP40 PEF1 TINAGL1 LOC105378626 TSSK3 MTMR9LP GC01M031668
GH01J031711 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.7 -68.6 -68570 4.8 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF48 SLC30A9 ZNF121 ZNF143 ADGRB2 PEF1 ENSG00000235790 LOC105378626 TINAGL1 SERINC2 COL16A1 SPOCD1 GC01P031741
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PEF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PEF1 gene promoter:

Genomic Locations for PEF1 Gene

Genomic Locations for PEF1 Gene
chr1:31,629,862-31,645,237
(GRCh38/hg38)
Size:
15,376 bases
Orientation:
Minus strand
chr1:32,095,463-32,110,838
(GRCh37/hg19)

Genomic View for PEF1 Gene

Genes around PEF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PEF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PEF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PEF1 Gene

Proteins for PEF1 Gene

  • Protein details for PEF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBV8-PEF1_HUMAN
    Recommended name:
    Peflin
    Protein Accession:
    Q9UBV8

    Protein attributes for PEF1 Gene

    Size:
    284 amino acids
    Molecular mass:
    30381 Da
    Quaternary structure:
    • Heterodimer; heterodimerizes (via the EF-hand 5) with PDCD6 (PubMed:11278427, PubMed:11883899, PubMed:27716508). Dissociates from PDCD6 in presence of calcium (PubMed:11278427).

neXtProt entry for PEF1 Gene

Post-translational modifications for PEF1 Gene

  • Ubiquitinated by the BCR(KLHL12) E3 ubiquitin ligase complex.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PEF1 Gene

No data available for DME Specific Peptides for PEF1 Gene

Domains & Families for PEF1 Gene

Gene Families for PEF1 Gene

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

Protein Domains for PEF1 Gene

Suggested Antigen Peptide Sequences for PEF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PEF1: view

No data available for UniProtKB/Swiss-Prot for PEF1 Gene

Function for PEF1 Gene

Molecular function for PEF1 Gene

UniProtKB/Swiss-Prot Function:
Calcium-binding protein that acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium. Together with PDCD6, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in endoplasmic reticulum (ER)-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PDCD6 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Its role in the heterodimer formed with PDCD6 is however unclear: some evidences show that PEF1 and PDCD6 work together and promote association between PDCD6 and SEC31 in presence of calcium (PubMed:27716508). Other reports show that PEF1 dissociates from PDCD6 in presence of calcium, and may act as a negative regulator of PDCD6 (PubMed:11278427). Also acts as a negative regulator of ER-Golgi transport; possibly by inhibiting interaction between PDCD6 and SEC31 (By similarity).

Phenotypes From GWAS Catalog for PEF1 Gene

Gene Ontology (GO) - Molecular Function for PEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0004198 calcium-dependent cysteine-type endopeptidase activity IBA --
GO:0005509 calcium ion binding IEA,TAS --
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PEF1: view
genes like me logo Genes that share phenotypes with PEF1: view

Animal Model Products

CRISPR Products

miRNA for PEF1 Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PEF1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PEF1 Gene

Localization for PEF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PEF1 Gene

Cytoplasm. Endoplasmic reticulum. Membrane; Peripheral membrane protein. Cytoplasmic vesicle, COPII-coated vesicle membrane; Peripheral membrane protein. Note=Membrane-associated in the presence of Ca(2+) (PubMed:11278427). Localizes to endoplasmic reticulum exit site (ERES) (By similarity). {ECO:0000250 UniProtKB:Q641Z8, ECO:0000269 PubMed:11278427}.

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 PEF1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
cytosol 3
nucleus 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (3)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IDA,IEA 11278427
GO:0005783 endoplasmic reticulum IEA --
GO:0012507 ER to Golgi transport vesicle membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PEF1: view

Pathways & Interactions for PEF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IBA --
GO:0006888 ER to Golgi vesicle-mediated transport IMP 27716508
GO:0014029 neural crest formation IMP 27716508
GO:0014032 neural crest cell development IMP 27716508
GO:0048208 COPII vesicle coating IMP 27716508
genes like me logo Genes that share ontologies with PEF1: view

No data available for Pathways by source and SIGNOR curated interactions for PEF1 Gene

Drugs & Compounds for PEF1 Gene

(2) Drugs for PEF1 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Citrate Approved Pharma Target, ligand 0
Calcium Phosphate Approved Pharma Target, ligand 0
genes like me logo Genes that share compounds with PEF1: view

Transcripts for PEF1 Gene

mRNA/cDNA for PEF1 Gene

(10) Additional mRNA sequences :
(7) REFSEQ mRNAs :
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PEF1 Gene

Penta-EF-hand domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PEF1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PEF1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c · 8d · 8e · 8f
SP1: - - - - - - - - -
SP2: - - - - - - - - - -
SP3: - - - -
SP4: - - - - - - - - - - - - -
SP5: - - - - -
SP6:
SP7: -
SP8: - - - - - - - - - - - -
SP9: - -
SP10: -

Relevant External Links for PEF1 Gene

GeneLoc Exon Structure for
PEF1
ECgene alternative splicing isoforms for
PEF1

Expression for PEF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PEF1 Gene

Protein differential expression in normal tissues from HIPED for PEF1 Gene

This gene is overexpressed in Bone (7.8) and Urine (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PEF1 Gene



Protein tissue co-expression partners for PEF1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PEF1 Gene:

PEF1

SOURCE GeneReport for Unigene cluster for PEF1 Gene:

Hs.470417

Evidence on tissue expression from TISSUES for PEF1 Gene

  • Nervous system(4.5)
  • Skin(4.3)
  • Spleen(4.3)
  • Lung(2.7)
genes like me logo Genes that share expression patterns with PEF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PEF1 Gene

Orthologs for PEF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PEF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PEF1 34 33
  • 99.88 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PEF1 34 33
  • 90.56 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pef1 16 34 33
  • 85.45 (n)
cow
(Bos Taurus)
Mammalia PEF1 34 33
  • 84.98 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PEF1 34
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pef1 33
  • 81.86 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PEF1 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PEF1 34 33
  • 76.65 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PEF1 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pef1 33
  • 70.49 (n)
zebrafish
(Danio rerio)
Actinopterygii pef1 34 33
  • 65.78 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006246 33
  • 54.61 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17765 34 33
  • 54.44 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PEF1 34
  • 19 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G10300 33
  • 46.34 (n)
rice
(Oryza sativa)
Liliopsida Os12g0137100 33
  • 48.86 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4642 34
  • 45 (a)
OneToOne
Species where no ortholog for PEF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PEF1 Gene

ENSEMBL:
Gene Tree for PEF1 (if available)
TreeFam:
Gene Tree for PEF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PEF1: view image

Paralogs for PEF1 Gene

Paralogs for PEF1 Gene

(2) SIMAP similar genes for PEF1 Gene using alignment to 2 proteins:

  • PEF1_HUMAN
  • E7ETX1_HUMAN

Pseudogenes.org Pseudogenes for PEF1 Gene

genes like me logo Genes that share paralogs with PEF1: view

Variants for PEF1 Gene

Sequence variations from dbSNP and Humsavar for PEF1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000078239 -- 31,638,873(-) C/T intron_variant
rs1000112926 -- 31,647,106(-) C/T upstream_transcript_variant
rs1000251485 -- 31,634,903(-) T/C 5_prime_UTR_variant, intron_variant
rs1000298287 -- 31,642,193(-) A/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000494561 -- 31,646,988(-) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PEF1 Gene

Variant ID Type Subtype PubMed ID
esv2758930 CNV loss 17122850
nsv1000976 CNV loss 25217958
nsv470708 CNV loss 18288195
nsv545951 CNV gain 21841781

Variation tolerance for PEF1 Gene

Residual Variation Intolerance Score: 42.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.70; 32.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PEF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PEF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PEF1 Gene

Disorders for PEF1 Gene

Additional Disease Information for PEF1

No disorders were found for PEF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PEF1 Gene

Publications for PEF1 Gene

  1. Both ALG-2 and peflin, penta-EF-hand (PEF) proteins, are stabilized by dimerization through their fifth EF-hand regions. (PMID: 11883899) Kitaura Y … Maki M (Archives of biochemistry and biophysics 2002) 2 3 4 22 58
  2. Peflin, a novel member of the five-EF-hand-protein family, is similar to the apoptosis-linked gene 2 (ALG-2) protein but possesses nonapeptide repeats in the N-terminal hydrophobic region. (PMID: 10486255) Kitaura Y … Maki M (Biochemical and biophysical research communications 1999) 2 3 4 22 58
  3. Peflin and ALG-2, members of the penta-EF-hand protein family, form a heterodimer that dissociates in a Ca2+-dependent manner. (PMID: 11278427) Kitaura Y … Maki M (The Journal of biological chemistry 2001) 3 4 22 58
  4. Regulation of the CUL3 Ubiquitin Ligase by a Calcium-Dependent Co-adaptor. (PMID: 27716508) McGourty CA … Rape M (Cell 2016) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for PEF1 Gene

Sources for PEF1 Gene

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