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    PIP5K1C phosphatidylinositol-4-phosphate 5-kinase type 1 gamma [ Homo sapiens (human) ]

    Gene ID: 23396, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PIP5K1Cprovided by HGNC
    Official Full Name
    phosphatidylinositol-4-phosphate 5-kinase type 1 gammaprovided by HGNC
    Primary source
    HGNC:HGNC:8996
    See related
    Ensembl:ENSG00000186111 MIM:606102; AllianceGenome:HGNC:8996
    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
    LCCS3; PIP5Kgamma; PIP5K-GAMMA; PIP5K1-gamma
    Summary
    This locus encodes a type I phosphatidylinositol 4-phosphate 5-kinase. The encoded protein catalyzes phosphorylation of phosphatidylinositol 4-phosphate, producing phosphatidylinositol 4,5-bisphosphate. This enzyme is found at synapses and has been found to play roles in endocytosis and cell migration. Mutations at this locus have been associated with lethal congenital contractural syndrome. Alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Sep 2010]
    Expression
    Broad expression in testis (RPKM 14.7), brain (RPKM 13.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PIP5K1C in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3630183..3700468, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3608310..3678870, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3630181..3700466, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3605850-3606424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3606998-3607571 Neighboring gene thromboxane A2 receptor Neighboring gene CACTIN antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3618043-3618915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3623949-3624450 Neighboring gene cactin, spliceosome C complex subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3624451-3624950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3625177-3625738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3625739-3626300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:3626301-3626862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3643569-3644108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3644109-3644646 Neighboring gene MPRA-validated peak3250 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3665265-3666095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3672153-3672828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3673765-3674558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3675389-3675890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3679833-3680333 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3681521-3682070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3682071-3682618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3682619-3683168 Neighboring gene Sharpr-MPRA regulatory region 323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13743 Neighboring gene Sharpr-MPRA regulatory region 5698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3699523-3700306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3707827-3708490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3708491-3709152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3709988-3710533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3712547-3713048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3713049-3713548 Neighboring gene tight junction protein 3 Neighboring gene MPRA-validated peak3252 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3761575-3761892 Neighboring gene uncharacterized LOC105372248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13744 Neighboring gene amyloid beta precursor protein binding family A member 3

    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. Lethal contractural syndrome type 3 (LCCS3) is caused by a mutation in PIP5K1C, which encodes PIPKI gamma of the phophatidylinsitol pathway. Narkis G, et al. Am J Hum Genet, 2007 Sep. PMID 17701898, Free PMC Article
    2. Cdk5-mediated phosphorylation regulates phosphatidylinositol 4-phosphate 5-kinase type I γ 90 activity and cell invasion. Li L, et al. FASEB J, 2019 Jan. PMID 30040488, Free PMC Article
    3. Type Iγ phosphatidylinositol phosphate kinase promotes tumor growth by facilitating Warburg effect in colorectal cancer. Peng W, et al. EBioMedicine, 2019 Jun. PMID 31105034, Free PMC Article
    4. PIPKIγ Regulates CCL2 Expression in Colorectal Cancer by Activating AKT-STAT3 Signaling. Xue J, et al. J Immunol Res, 2019. PMID 31781676, Free PMC Article
    5. Type I gamma phosphatidylinositol phosphate kinase modulates invasion and proliferation and its expression correlates with poor prognosis in breast cancer. Sun Y, et al. Breast Cancer Res, 2010. PMID 20074374, Free PMC Article

    See all (87) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Temporal involvement of phosphatidylinositol 4-phosphate 5-kinase gamma in differentiation of Z-bands and myofilament bundles as well as intercalated discs in mouse heart at mid-gestation.
      Title: Temporal involvement of phosphatidylinositol 4-phosphate 5-kinase γ in differentiation of Z-bands and myofilament bundles as well as intercalated discs in mouse heart at mid-gestation.
    2. Type I gamma phosphatidylinositol phosphate 5-kinase i5 controls cell sensitivity to interferon.
      Title: Type I gamma phosphatidylinositol phosphate 5-kinase i5 controls cell sensitivity to interferon.
    3. CLIC1 recruits PIP5K1A/C to induce cell-matrix adhesions for tumor metastasis.
      Title: CLIC1 recruits PIP5K1A/C to induce cell-matrix adhesions for tumor metastasis.
    4. Type I Phosphatidylinositol-4-Phosphate 5-Kinases alpha and gamma Play a Key Role in Targeting HIV-1 Pr55(Gag) to the Plasma Membrane.
      Title: Type I Phosphatidylinositol-4-Phosphate 5-Kinases α and γ Play a Key Role in Targeting HIV-1 Pr55(Gag) to the Plasma Membrane.
    5. our observations revealed that high PIPKIgamma expression in tumor cells could induce AKT-mTOR signaling activation. Increased activation of AKT-mTOR increases the phosphorylation levels of STAT3, leading to CCL2 expression and suppressing cancer immune reaction activation.
      Title: PIPKIγ Regulates CCL2 Expression in Colorectal Cancer by Activating AKT-STAT3 Signaling.
    6. Our findings reveal a new regulatory role of PIPKIgamma in Warburg effect and provide a key contributor in colorectal cancer metabolism with potential therapeutic potentials.
      Title: Type Iγ phosphatidylinositol phosphate kinase promotes tumor growth by facilitating Warburg effect in colorectal cancer.
    7. PIP5K1C was significantly associated with Alcohol Use Disorder in the African ancestry group. However, a replication analysis using an independent sample (N = 3,801) found no significant associations after correction for multiple testing.
      Title: Genetic Association and Expression Analyses of the Phosphatidylinositol-4-Phosphate 5-Kinase (PIP5K1C) Gene in Alcohol Use Disorder-Relevance for Pain Signaling and Alcohol Use.
    8. Cdk5-mediated PIPKIgamma90 phosphorylation is essential for cell invasion leading to breast cancer.
      Title: Cdk5-mediated phosphorylation regulates phosphatidylinositol 4-phosphate 5-kinase type I γ 90 activity and cell invasion.
    9. The Btk-dependent PIP5K1gamma lipid kinase activation by Fas counteracts FasL-induced cell death.
      Title: The Btk-dependent PIP5K1γ lipid kinase activation by Fas counteracts FasL-induced cell death.
    10. High expression of PIP5K1-gamma is associated with colorectal cancer.
      Title: Silencing of type Iγ phosphatidylinositol phosphate kinase suppresses ovarian cancer cell proliferation, migration and invasion.
    Submit: New GeneRIF Correction See all GeneRIFs (42)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Lethal congenital contracture syndrome 3
    MedGen: C1969655 OMIM: 611369 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of phosphatidylinositol-4-phosphate 5-kinase, type I, gamma (PIP5K1C) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • KIAA0589

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 1-phosphatidylinositol-4-phosphate 5-kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 1-phosphatidylinositol-4-phosphate 5-kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol kinase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in adherens junction assembly TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cell-cell adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in clathrin-dependent endocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in membrane organization TAS
    Traceable Author Statement
    more info
    		  
    involved_in neutrophil chemotaxis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in phagocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphatidylinositol phosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction TAS
    Traceable Author Statement
    more info
    		  
    involved_in synaptic vesicle endocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic vesicle exocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in adherens junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in focal adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in phagocytic cup IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ruffle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in uropod TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phosphatidylinositol 4-phosphate 5-kinase type-1 gamma
    Names
    PIP5K1gamma
    diphosphoinositide kinase
    phosphatidylinositol-4-phosphate 5-kinase, type I, gamma
    ptdIns(4)P-5-kinase 1 gamma
    type I PIP kinase
    type I phosphatidylinositol 4-phosphate 5-kinase gamma
    NP_001182662.1
    NP_001287778.1
    NP_036530.1
    XP_011526150.1
    XP_011526151.1
    XP_016882029.1
    XP_047294489.1
    XP_047294490.1
    XP_047294491.1
    XP_047294492.1
    XP_047294493.1
    XP_054176363.1
    XP_054176364.1
    XP_054176365.1
    XP_054176366.1
    XP_054176367.1
    XP_054176368.1
    XP_054176369.1
    XP_054176370.1

    NCBI Reference Sequences (RefSeq)

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    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_012161.2 RefSeqGene

      Range
      4980..75265
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001195733.2 → NP_001182662.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1, also known as PIPKIgamma640 and PIPKIgamma87).
      Source sequence(s)
      AB011161, AK315912, BC011138, DC389567
      Consensus CDS
      CCDS56074.1
      UniProtKB/TrEMBL
      B4DVZ9
      Related
      ENSP00000445992.1, ENST00000539785.5
      Conserved Domains (1) summary
      cd17308
      Location:76 → 449
      PIPKc_PIP5K1C; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins

    2. NM_001300849.2 → NP_001287778.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform 3

      See identical proteins and their annotated locations for NP_001287778.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as PIPKIgamma_v5) encodes the longest isoform (3, also known as PIPKIgamma_i5).
      Source sequence(s)
      FJ965537, HY000479
      Consensus CDS
      CCDS74257.1
      UniProtKB/TrEMBL
      B4DVZ9
      Related
      ENSP00000466363.1, ENST00000589578.5
      Conserved Domains (2) summary
      PHA03151
      Location:497 → 672
      PHA03151; hypothetical protein; Provisional
      smart00330
      Location:103 → 443
      PIPKc; Phosphatidylinositol phosphate kinases

    3. NM_012398.3 → NP_036530.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform 2

      See identical proteins and their annotated locations for NP_036530.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate, in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2, also known as PIPKIgamma668 and PIPKIgamma90) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AB011161, AK315912, BC011138, DC389567
      Consensus CDS
      CCDS32872.1
      UniProtKB/Swiss-Prot
      B7Z9E7, C6GIJ7, C6GIJ8, O60331, Q7LE07
      UniProtKB/TrEMBL
      B4DVZ9
      Related
      ENSP00000335333.3, ENST00000335312.8
      Conserved Domains (1) summary
      cd17308
      Location:76 → 449
      PIPKc_PIP5K1C; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      3630183..3700468 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438535.1 → XP_047294491.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X6

      UniProtKB/TrEMBL
      B4DVZ9

    2. XM_017026540.3 → XP_016882029.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X4

      UniProtKB/TrEMBL
      B4DVZ9

    3. XM_011527849.2 → XP_011526151.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X5

      UniProtKB/TrEMBL
      B4DVZ9
      Conserved Domains (1) summary
      smart00330
      Location:103 → 443
      PIPKc; Phosphatidylinositol phosphate kinases

    4. XM_011527848.2 → XP_011526150.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X3

      UniProtKB/TrEMBL
      B4DVZ9
      Conserved Domains (2) summary
      PHA03151
      Location:497 → 665
      PHA03151; hypothetical protein; Provisional
      cd17308
      Location:76 → 449
      PIPKc_PIP5K1C; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins

    5. XM_047438533.1 → XP_047294489.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X1

      UniProtKB/TrEMBL
      B4DVZ9
      Related
      ENSP00000444779.1, ENST00000537021.1

    6. XM_047438534.1 → XP_047294490.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X2

      UniProtKB/TrEMBL
      B4DVZ9

    7. XM_047438536.1 → XP_047294492.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X7

      UniProtKB/TrEMBL
      B4DVZ9

    8. XM_047438537.1 → XP_047294493.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      3608310..3678870 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320393.1 → XP_054176368.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X6

      UniProtKB/TrEMBL
      B4DVZ9

    2. XM_054320391.1 → XP_054176366.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X4

      UniProtKB/TrEMBL
      B4DVZ9

    3. XM_054320392.1 → XP_054176367.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X5

      UniProtKB/TrEMBL
      B4DVZ9

    4. XM_054320390.1 → XP_054176365.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X3

      UniProtKB/TrEMBL
      B4DVZ9

    5. XM_054320388.1 → XP_054176363.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X1

      UniProtKB/TrEMBL
      B4DVZ9

    6. XM_054320389.1 → XP_054176364.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X2

      UniProtKB/TrEMBL
      B4DVZ9

    7. XM_054320394.1 → XP_054176369.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X7

      UniProtKB/TrEMBL
      B4DVZ9

    8. XM_054320395.1 → XP_054176370.1  phosphatidylinositol 4-phosphate 5-kinase type-1 gamma isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60331.2 GenPept UniProtKB/Swiss-Prot:O60331

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