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PPEF1 protein phosphatase with EF-hand domain 1 [ Homo sapiens (human) ]

Gene ID: 5475, updated on 3-Apr-2024

Summary

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Official Symbol
PPEF1provided by HGNC
Official Full Name
protein phosphatase with EF-hand domain 1provided by HGNC
Primary source
HGNC:HGNC:9243
See related
Ensembl:ENSG00000086717 MIM:300109; AllianceGenome:HGNC:9243
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
PP7; PPEF; PPP7C; PPP7CA
Summary
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]
Expression
Biased expression in testis (RPKM 8.3) and brain (RPKM 1.3) See more
Orthologs
mouse all
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Genomic context

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Location:
Xp22.13
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18675067..18827917)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (18257672..18410535)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18693187..18846035)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene cyclin dependent kinase like 5 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18658784-18658953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18667451-18668199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18679457-18680008 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18693026-18693212 Neighboring gene tRNA-Val (anticodon TAC) 1-2 Neighboring gene retinoschisin 1 Neighboring gene PPEF1 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:18811885-18812468 Neighboring gene uncharacterized LOC124905254 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:18851133-18852056 Neighboring gene BLOC1S6 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29459 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:18880662-18881162 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:18881163-18881663 Neighboring gene HAUS augmin like complex subunit 1 pseudogene 2

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. Molecular cloning of a novel PPEF-1 gene variant from a T-cell lymphoblastic lymphoma cell line. Ho P, et al. Recent Pat DNA Gene Seq, 2012 Apr. PMID 22292511
  2. Effects of serine/threonine protein phosphatases on ion channels in excitable membranes. Herzig S, et al. Physiol Rev, 2000 Jan. PMID 10617768
  3. Molecular cloning, expression, and characterization of a novel human serine/threonine protein phosphatase, PP7, that is homologous to Drosophila retinal degeneration C gene product (rdgC). Huang X, et al. J Biol Chem, 1998 Jan 16. PMID 9430683
  4. The protein phosphatase with EF-hand domain 1 is a calmodulin-binding protein that interacts with proteins involved in sperm capacitation, binding to the zona pellucida, and motility. Lavoie-Ouellet C, et al. Mol Reprod Dev, 2021 Apr. PMID 33783058
  5. Protein serine/threonine phosphatase PPEF-1 suppresses genotoxic stress response via dephosphorylation of PDCD5. Park SY, et al. Sci Rep, 2017 Jan 4. PMID 28051100, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The protein phosphatase with EF-hand domain 1 is a calmodulin-binding protein that interacts with proteins involved in sperm capacitation, binding to the zona pellucida, and motility.
    Title: The protein phosphatase with EF-hand domain 1 is a calmodulin-binding protein that interacts with proteins involved in sperm capacitation, binding to the zona pellucida, and motility.
  2. Collectively, these data demonstrate that PPEF-1 plays a pivotal role in tumorigenesis of lung cancer cells by reducing PDCD5-mediated genotoxic stress responses.
    Title: Protein serine/threonine phosphatase PPEF-1 suppresses genotoxic stress response via dephosphorylation of PDCD5.
  3. PPEF-1V is a 350bp deletion in the nucleotide sequence of PPEF-1 from 128-477bp and a 152-amino-acid N-terminal deletion in the amino acid sequence of PPEF-1.
    Title: Molecular cloning of a novel PPEF-1 gene variant from a T-cell lymphoblastic lymphoma cell line.
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)

Genotypes

Pathways from PubChem

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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 calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables iron ion binding IEA
Inferred from Electronic Annotation
more info
  
enables manganese ion binding IEA
Inferred from Electronic Annotation
more info
  
enables myosin phosphatase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein serine/threonine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in detection of stimulus involved in sensory perception IEA
Inferred from Electronic Annotation
more info
  
involved_in protein dephosphorylation TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
serine/threonine-protein phosphatase with EF-hands 1
Names
protein phosphatase 7, catalytic subunit, alpha isozyme
protein phosphatase with EF calcium-binding domain
protein phosphatase, EF-hand calcium binding domain 1
protein phosphatase, serine/threonine type, with EF-hands
serine/threonine protein phosphatase 7
NP_001364915.1
NP_001364922.1
NP_001364923.1
NP_001364924.1
NP_001364925.1
NP_001365310.1
NP_001365311.1
NP_001376549.1
NP_001376550.1
NP_001376552.1
NP_001376553.1
NP_006231.2
NP_689410.1
NP_689412.1
XP_016885101.1
XP_047298148.1
XP_047298149.1
XP_047298150.1
XP_047298151.1
XP_054183261.1
XP_054183262.1
XP_054183263.1
XP_054183264.1
XP_054183265.1

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.

Genomic

  1. NG_012519.2 RefSeqGene

    Range
    37580..157852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001377986.2 → NP_001364915.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  2. NM_001377993.1 → NP_001364922.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Related
    ENSP00000510505.1, ENST00000692488.1
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  3. NM_001377994.1 → NP_001364923.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    UniProtKB/TrEMBL
    B7Z353, B7Z6R7
    Conserved Domains (2) summary
    cd07420
    Location:50 → 387
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:503 → 571
    EF-hand_7; EF-hand domain pair

  4. NM_001377995.1 → NP_001364924.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS94563.1
    UniProtKB/TrEMBL
    A0A8I5KXD3, B7Z353
    Conserved Domains (3) summary
    PTZ00183
    Location:395 → 543
    PTZ00183; centrin; Provisional
    cd07420
    Location:25 → 362
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:478 → 546
    EF-hand_7; EF-hand domain pair

  5. NM_001377996.1 → NP_001364925.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Related
    ENSP00000419273.2, ENST00000470157.2
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  6. NM_001378381.1 → NP_001365310.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  7. NM_001378382.1 → NP_001365311.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    UniProtKB/TrEMBL
    B0AZL8
    Conserved Domains (4) summary
    PTZ00183
    Location:393 → 541
    PTZ00183; centrin; Provisional
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    pfam13499
    Location:476 → 544
    EF-hand_7; EF-hand domain pair
    cl13995
    Location:79 → 360
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain

  8. NM_001389620.1 → NP_001376549.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  9. NM_001389621.1 → NP_001376550.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Related
    ENSP00000509623.1, ENST00000471570.6
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  10. NM_001389623.1 → NP_001376552.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS43920.1
    UniProtKB/TrEMBL
    B0AZL8
    Related
    ENSP00000341892.5, ENST00000349874.10
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    pfam13499
    Location:506 → 574
    EF-hand_7; EF-hand domain pair
    cl13995
    Location:115 → 390
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain

  11. NM_001389624.1 → NP_001376553.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS94563.1
    UniProtKB/TrEMBL
    A0A8I5KXD3, B7Z353
    Related
    ENSP00000508824.1, ENST00000496616.6
    Conserved Domains (3) summary
    PTZ00183
    Location:395 → 543
    PTZ00183; centrin; Provisional
    cd07420
    Location:25 → 362
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:478 → 546
    EF-hand_7; EF-hand domain pair

  12. NM_006240.4 → NP_006231.2  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

    See identical proteins and their annotated locations for NP_006231.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the predominant isoform (1).
    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS14188.1
    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    UniProtKB/TrEMBL
    B0AZL8
    Related
    ENSP00000354871.3, ENST00000361511.9
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    cd07420
    Location:115 → 452
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:568 → 636
    EF-hand_7; EF-hand domain pair

  13. NM_152224.2 → NP_689410.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1b

    See identical proteins and their annotated locations for NP_689410.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1b) uses an alternate in-frame splice site compared to variant 1, resulting in an isoform (1b) that lacks an internal segment compared to isoform 1. Isoform 1b contains a catalytic domain and two EF-hand motifs. Its functional significance is unknown.
    Source sequence(s)
    AL096700, Z94056
    UniProtKB/TrEMBL
    B0AZL8
    Conserved Domains (5) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    smart00156
    Location:134 → 427
    PP2Ac; Protein phosphatase 2A homologues, catalytic domain
    cd00051
    Location:542 → 607
    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 ...
    cd07420
    Location:115 → 424
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:546 → 607
    EF-hand_7; EF-hand domain pair

  14. NM_152226.2 → NP_689412.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 3

    See identical proteins and their annotated locations for NP_689412.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the coding region compared to variant 1, resulting in an isoform (3) that is missing an internal segment compared to isoform 1. Isoform 3 contains a catalytic domain and two EF-hand motifs. Its functional significance is unknown.
    Source sequence(s)
    AL096700, Z94056
    Consensus CDS
    CCDS43920.1
    UniProtKB/TrEMBL
    B0AZL8
    Conserved Domains (3) summary
    smart00015
    Location:18 → 37
    IQ; Calmodulin-binding motif
    pfam13499
    Location:506 → 574
    EF-hand_7; EF-hand domain pair
    cl13995
    Location:115 → 390
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    18675067..18827917
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442194.1 → XP_047298150.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

  2. XM_047442195.1 → XP_047298151.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

  3. XM_047442193.1 → XP_047298149.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
    Related
    ENSP00000509616.1, ENST00000689646.1

  4. XM_017029612.2 → XP_016885101.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

    UniProtKB/TrEMBL
    A0A8I5KXD3, B7Z353
    Conserved Domains (3) summary
    PTZ00183
    Location:395 → 543
    PTZ00183; centrin; Provisional
    cd07420
    Location:25 → 362
    MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
    pfam13499
    Location:478 → 546
    EF-hand_7; EF-hand domain pair

  5. XM_047442192.1 → XP_047298148.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    18257672..18410535
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327288.1 → XP_054183263.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

  2. XM_054327289.1 → XP_054183264.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

  3. XM_054327287.1 → XP_054183262.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

  4. XM_054327290.1 → XP_054183265.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

    UniProtKB/TrEMBL
    A0A8I5KXD3

  5. XM_054327286.1 → XP_054183261.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

    UniProtKB/Swiss-Prot
    A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152223.1: Suppressed sequence

    Description
    NM_152223.1: This RefSeq was permanently suppressed because it contains the wrong CDS. Annotation of the correct CDS causes this transcript to be a candidate for nonsense-mediated mRNA decay (NMD).

  2. NM_152225.1: Suppressed sequence

    Description
    NM_152225.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14829.1 GenPept UniProtKB/Swiss-Prot:O14829

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