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

    Gene ID: 5475, updated on 10-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    See PPEF1 in Genome Data Viewer
    Location:
    Xp22.13
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18675067..18827917)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (18257672..18410535)
    RS_2024_09 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

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    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

    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)

    NEW Try the new Transcript table

    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_001377986.2NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    2. NM_001377993.1NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    3. NM_001377994.1NP_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:50387
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:503571
      EF-hand_7; EF-hand domain pair
    4. NM_001377995.1NP_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:395543
      PTZ00183; centrin; Provisional
      cd07420
      Location:25362
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:478546
      EF-hand_7; EF-hand domain pair
    5. NM_001377996.1NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    6. NM_001378381.1NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    7. NM_001378382.1NP_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:393541
      PTZ00183; centrin; Provisional
      smart00015
      Location:1837
      IQ; Calmodulin-binding motif
      pfam13499
      Location:476544
      EF-hand_7; EF-hand domain pair
      cl13995
      Location:79360
      MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
    8. NM_001389620.1NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    9. NM_001389621.1NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    10. NM_001389623.1NP_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:1837
      IQ; Calmodulin-binding motif
      pfam13499
      Location:506574
      EF-hand_7; EF-hand domain pair
      cl13995
      Location:115390
      MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
    11. NM_001389624.1NP_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:395543
      PTZ00183; centrin; Provisional
      cd07420
      Location:25362
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:478546
      EF-hand_7; EF-hand domain pair
    12. NM_006240.4NP_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:1837
      IQ; Calmodulin-binding motif
      cd07420
      Location:115452
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:568636
      EF-hand_7; EF-hand domain pair
    13. NM_152224.2NP_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:1837
      IQ; Calmodulin-binding motif
      smart00156
      Location:134427
      PP2Ac; Protein phosphatase 2A homologues, catalytic domain
      cd00051
      Location:542607
      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:115424
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:546607
      EF-hand_7; EF-hand domain pair
    14. NM_152226.2NP_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:1837
      IQ; Calmodulin-binding motif
      pfam13499
      Location:506574
      EF-hand_7; EF-hand domain pair
      cl13995
      Location:115390
      MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain

    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

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8
    2. XM_047442195.1XP_047298151.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8
    3. XM_047442193.1XP_047298149.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8
      Related
      ENSP00000509616.1, ENST00000689646.1
    4. XM_017029612.2XP_016885101.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KXD3, B7Z353
      Conserved Domains (3) summary
      PTZ00183
      Location:395543
      PTZ00183; centrin; Provisional
      cd07420
      Location:25362
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:478546
      EF-hand_7; EF-hand domain pair
    5. XM_047442192.1XP_047298148.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8

    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_054327288.1XP_054183263.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8
    2. XM_054327289.1XP_054183264.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8
    3. XM_054327287.1XP_054183262.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8
    4. XM_054327290.1XP_054183265.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KXD3, B7Z353
    5. XM_054327286.1XP_054183261.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      UniProtKB/Swiss-Prot
      A6NHP4, A8K348, O14829, O15253, Q9NU21, Q9UJH0
      UniProtKB/TrEMBL
      B0AZL8

    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.