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

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; 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: mouse all
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Genomic context

Location:: 1p35.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (31629866..31644876, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (31487512..31502526, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (32095467..32110477, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH79572 (e-PCR)
- UniSTS:92816

D1S1472 (e-PCR)
- UniSTS:149668

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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 more info	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)

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
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

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

31629866..31644876 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DVT7