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PEF1 penta-EF-hand domain containing 1 [ Homo sapiens (human) ]

Gene ID: 553115, updated on 11-Apr-2024

Summary

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Official Symbol
PEF1provided by HGNC
Official Full Name
penta-EF-hand domain containing 1provided by HGNC
Primary source
HGNC:HGNC:30009
See related
Ensembl:ENSG00000162517 MIM:610033; AllianceGenome:HGNC:30009
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ABP32; PEF1A
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 29.9), placenta (RPKM 14.6) and 25 other tissues See more
Orthologs
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Genomic context

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See PEF1 in Genome Data Viewer
Location:
1p35.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31629866..31644876, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31487512..31502526, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32095467..32110477, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903917 Neighboring gene Sharpr-MPRA regulatory region 14090 Neighboring gene uncharacterized LOC105378626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32034359-32034860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32041927-32042647 Neighboring gene tubulointerstitial nephritis antigen like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 571 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:32070860-32072059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32080194-32080980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32083206-32083895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090464-32090964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32090965-32091465 Neighboring gene hypocretin receptor 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32110207-32110977 Neighboring gene PEF1 and COL16A1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32123622-32123860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32124291-32124792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131402-32131941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32131942-32132480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32133021-32133558 Neighboring gene collagen type XVI alpha 1 chain Neighboring gene uncharacterized LOC101929444 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:32145564-32146763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32147039-32147911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32162063-32162572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32164717-32165470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32166977-32167729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 649 Neighboring gene Sharpr-MPRA regulatory region 11964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32181521-32182116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32189409-32189910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 573 Neighboring gene adhesion G protein-coupled receptor B2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32218779-32219393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32219394-32220007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32220374-32220980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32221586-32222191 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32222192-32222796 Neighboring gene microRNA 4254

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. 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. Kitaura Y, et al. Biochem Biophys Res Commun, 1999 Sep 16. PMID 10486255
  2. Penta-EF-Hand Protein Peflin Is a Negative Regulator of ER-To-Golgi Transport. Rayl M, et al. PLoS One, 2016. PMID 27276012, Free PMC Article
  3. Both ALG-2 and peflin, penta-EF-hand (PEF) proteins, are stabilized by dimerization through their fifth EF-hand regions. Kitaura Y, et al. Arch Biochem Biophys, 2002 Mar 1. PMID 11883899
  4. Peflin and ALG-2, members of the penta-EF-hand protein family, form a heterodimer that dissociates in a Ca2+-dependent manner. Kitaura Y, et al. J Biol Chem, 2001 Apr 27. PMID 11278427
  5. The PEF family proteins sorcin and grancalcin interact in vivo and in vitro. Hansen C, et al. FEBS Lett, 2003 Jun 19. PMID 12804766

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This work identifies for the first time a clear steady state role for a PEF protein in ER-to-Golgi transport-peflin is a negative regulator of transport.
    Title: Penta-EF-Hand Protein Peflin Is a Negative Regulator of ER-To-Golgi Transport.
  2. peflin is stabilized by dimerization through its fifth EF-hand region
    Title: Both ALG-2 and peflin, penta-EF-hand (PEF) proteins, are stabilized by dimerization through their fifth EF-hand regions.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables calcium-dependent protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin-like ligase-substrate adaptor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in COPII vesicle coating IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in COPII vesicle coating IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neural crest cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neural crest formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein monoubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to calcium ion IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
part_of COPII vesicle coat IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Cul3-RING ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 

General protein information

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Preferred Names
peflin
Names
PEF protein with a long N-terminal hydrophobic domain
epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001359651.2 → NP_001346580.1  peflin isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AC114488, BC012561, BI826532, CA307778, DB024828
    Conserved Domains (1) summary
    cd16184
    Location:48 → 213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins

  2. NM_012392.4 → NP_036524.1  peflin isoform 1

    See identical proteins and their annotated locations for NP_036524.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC114488, BC012561, CA307778
    Consensus CDS
    CCDS345.1
    UniProtKB/Swiss-Prot
    Q9UBV8
    UniProtKB/TrEMBL
    A0A384MQX5
    Related
    ENSP00000362807.4, ENST00000373703.5
    Conserved Domains (1) summary
    cd16184
    Location:118 → 283
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins

RNA

  1. NR_033686.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC114488, BC012561, BG546473, CA307778

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    31629866..31644876 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541745.2 → XP_011540047.1  peflin isoform X1

    Conserved Domains (3) summary
    cd00051
    Location:118 → 176
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:118 → 174
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:182 → 273
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

  2. XM_017001680.2 → XP_016857169.1  peflin isoform X2

    Conserved Domains (1) summary
    cd16184
    Location:48 → 213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins

  3. XM_011541747.2 → XP_011540049.1  peflin isoform X2

    See identical proteins and their annotated locations for XP_011540049.1

    Conserved Domains (1) summary
    cd16184
    Location:48 → 213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins

  4. XM_011541746.3 → XP_011540048.1  peflin isoform X2

    See identical proteins and their annotated locations for XP_011540048.1

    Conserved Domains (1) summary
    cd16184
    Location:48 → 213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins

  5. XM_017001681.2 → XP_016857170.2  peflin isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31487512..31502526 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337501.1 → XP_054193476.1  peflin isoform X1

  2. XM_054337504.1 → XP_054193479.1  peflin isoform X2

  3. XM_054337503.1 → XP_054193478.1  peflin isoform X2

  4. XM_054337502.1 → XP_054193477.1  peflin isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UBV8.1 GenPept UniProtKB/Swiss-Prot:Q9UBV8

Gene LinkOut

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