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

    Gene ID: 5475, updated on 2-Nov-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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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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, 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
    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 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
    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_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_047442194.1 → 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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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