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

Gene ID: 553115, updated on 5-Apr-2020

Summary

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
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

Genomic context

See PEF1 in Genome Data Viewer
Location:
1p35.2
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (31629862..31644876, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32095463..32110838, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1226 Neighboring gene uncharacterized LOC105378626 Neighboring gene tubulointerstitial nephritis antigen like 1 Neighboring gene hypocretin receptor 1 Neighboring gene uncharacterized LOC105378628 Neighboring gene PEF1 and COL16A1 antisense RNA 1 Neighboring gene collagen type XVI alpha 1 chain Neighboring gene uncharacterized LOC101929444

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001359651.1NP_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:48213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins
  2. NM_012392.4NP_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
    Related
    ENSP00000362807.4, ENST00000373703.5
    Conserved Domains (1) summary
    cd16184
    Location:118283
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    31629862..31644876 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001681.1XP_016857170.1  peflin isoform X3

  2. XM_017001680.1XP_016857169.1  peflin isoform X2

    Conserved Domains (1) summary
    cd16184
    Location:48213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins
  3. XM_011541746.2XP_011540048.1  peflin isoform X2

    See identical proteins and their annotated locations for XP_011540048.1

    Conserved Domains (1) summary
    cd16184
    Location:48213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins
  4. XM_011541747.1XP_011540049.1  peflin isoform X2

    See identical proteins and their annotated locations for XP_011540049.1

    Conserved Domains (1) summary
    cd16184
    Location:48213
    EFh_PEF_peflin; EF-hand, calcium binding motif, found in peflin and similar proteins
  5. XM_011541745.1XP_011540047.1  peflin isoform X1

    Conserved Domains (3) summary
    cd00051
    Location:118176
    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:118174
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:182273
    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 ...
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