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pikfyve phosphoinositide kinase, FYVE finger containing [ Danio rerio (zebrafish) ]

Gene ID: 337690, updated on 27-Dec-2024

Summary

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Official Symbol
pikfyveprovided by ZNC
Official Full Name
phosphoinositide kinase, FYVE finger containingprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-9636
See related
Ensembl:ENSDARG00000056112 AllianceGenome:ZFIN:ZDB-GENE-030131-9636
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
pip5k3; wu:fo93c03
Summary
Predicted to enable 1-phosphatidylinositol-3-phosphate 5-kinase activity; ATP binding activity; and metal ion binding activity. Acts upstream of or within lens fiber cell morphogenesis and lysosomal transport. Located in membrane and perinuclear region of cytoplasm. Is expressed in several structures, including brain; digestive system; eye; muscle; and pleuroperitoneal region. Used to study cataract. Human ortholog(s) of this gene implicated in Fleck corneal dystrophy. Orthologous to human PIKFYVE (phosphoinositide kinase, FYVE-type zinc finger containing). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs
human mouse all
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Genomic context

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See pikfyve in Genome Data Viewer
Location:
chromosome: 9
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (32073673..32104183)
105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (32262917..32293453)

Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene fibroblast growth factor 14 Neighboring gene CFAP97 domain containing 2 Neighboring gene ankyrin repeat domain 44 Neighboring gene splicing factor 3b, subunit 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Inhibition of PIKfyve Leads to Lysosomal Disorders via Dysregulation of mTOR Signaling. Xia J, et al. Cells, 2024 May 30. PMID 38891085, Free PMC Article
  2. Characterization of pip5k3 fleck corneal dystrophy-linked gene in zebrafish. Boisset G, et al. Gene Expr Patterns, 2008 Jul. PMID 18558518
  3. Disruption of PIKFYVE causes congenital cataract in human and zebrafish. Mei S, et al. Elife, 2022 Jan 13. PMID 35023829, Free PMC Article
  4. The Lysosomal Storage Disorder Due to fig4a Mutation Causes Robust Liver Vacuolation in Zebrafish. Bao W, et al. Zebrafish, 2021 Jun. PMID 33909505
  5. Functional characterization and evolution of PTH/PTHrP receptors: insights from the chicken. Pinheiro PL, et al. BMC Evol Biol, 2012 Jul 6. PMID 22768871, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Inhibition of PIKfyve Leads to Lysosomal Disorders via Dysregulation of mTOR Signaling.
    Title: Inhibition of PIKfyve Leads to Lysosomal Disorders via Dysregulation of mTOR Signaling.
  2. Disruption of PIKFYVE causes congenital cataract in human and zebrafish.
    Title: Disruption of PIKFYVE causes congenital cataract in human and zebrafish.
  3. Cloning of pip5k3 and report on its molecular characterization and expression pattern in adult fish as well as during development.
    Title: Characterization of pip5k3 fleck corneal dystrophy-linked gene in zebrafish.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables 1-phosphatidylinositol-3-phosphate 5-kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within intracellular signal transduction IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within lens fiber cell morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within lysosomal transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within phosphatidylinositol metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in phosphatidylinositol metabolic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within phosphorylation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
1-phosphatidylinositol 3-phosphate 5-kinase
Names
phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III
NP_001120777.1
XP_005167723.1
XP_005167724.1
XP_005167726.1
XP_005167727.1
XP_009302997.1
XP_068079402.1
XP_068079403.1
XP_068079404.1

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.

mRNA and Protein(s)

  1. NM_001127305.1 → NP_001120777.1  1-phosphatidylinositol 3-phosphate 5-kinase

    See identical proteins and their annotated locations for NP_001120777.1

    Status: PROVISIONAL

    Source sequence(s)
    EU203547
    UniProtKB/TrEMBL
    A0A8M1NJJ1, A0A8M2BF26, B2KTE1, F6P813
    Related
    ENSDARP00000102577.1, ENSDART00000112453.3
    Conserved Domains (4) summary
    cd03334
    Location:644 → 904
    Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
    cd04448
    Location:383 → 464
    DEP_PIKfyve; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol ...
    cd15725
    Location:173 → 234
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:1820 → 2086
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007120.7 Reference GRCz11 Primary Assembly

    Range
    32073673..32104183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009304722.4 → XP_009302997.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X1

    UniProtKB/TrEMBL
    A0A8M3AW30, A0A8M3BCH5
    Conserved Domains (4) summary
    cd00139
    Location:1810 → 2104
    PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...
    cd03334
    Location:661 → 921
    Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
    cd04448
    Location:383 → 464
    DEP_PIKfyve; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol ...
    cd15725
    Location:173 → 234
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins

  2. XM_005167666.5 → XP_005167723.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X4

    See identical proteins and their annotated locations for XP_005167723.1

    UniProtKB/TrEMBL
    A0A8M1NJJ1, A0A8M2BF26, B2KTE1, F6P813
    Related
    ENSDARP00000099509.3, ENSDART00000110204.3
    Conserved Domains (4) summary
    cd03334
    Location:644 → 904
    Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
    cd04448
    Location:383 → 464
    DEP_PIKfyve; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol ...
    cd15725
    Location:173 → 234
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:1820 → 2086
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins

  3. XM_068223301.1 → XP_068079402.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X2

    UniProtKB/TrEMBL
    A0A8M3AW23

  4. XM_005167667.5 → XP_005167724.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X5

    See identical proteins and their annotated locations for XP_005167724.1

    UniProtKB/TrEMBL
    A0A8M2BF36, A0A8M3B2P6, B2KTE3, F1QGY6
    Related
    ENSDARP00000109122.3, ENSDART00000123278.5
    Conserved Domains (4) summary
    cd00139
    Location:1784 → 2078
    PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...
    cd03334
    Location:635 → 895
    Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
    cd04448
    Location:374 → 455
    DEP_PIKfyve; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol ...
    cd15725
    Location:173 → 234
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins

  5. XM_068223302.1 → XP_068079403.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X3

    UniProtKB/TrEMBL
    A0A8M3B5N9

  6. XM_005167669.5 → XP_005167726.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X6

    See identical proteins and their annotated locations for XP_005167726.1

    UniProtKB/TrEMBL
    A0A8M2BF26, B2KTE2
    Related
    ENSDARP00000149552.1, ENSDART00000180355.1
    Conserved Domains (4) summary
    cd00139
    Location:1777 → 2071
    PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...
    cd03334
    Location:628 → 888
    Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
    cd04448
    Location:367 → 448
    DEP_PIKfyve; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol ...
    cd15725
    Location:157 → 218
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins

  7. XM_005167670.5 → XP_005167727.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X7

    See identical proteins and their annotated locations for XP_005167727.1

    UniProtKB/TrEMBL
    A0A8M2BF52, A0A8M3B2P6, B2KTE4
    Related
    ENSDARP00000124842.1, ENSDART00000148767.3
    Conserved Domains (4) summary
    cd00139
    Location:1768 → 2062
    PIPKc; Phosphatidylinositol phosphate kinases (PIPK) catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. CD alignment includes type II ...
    cd03334
    Location:619 → 879
    Fab1_TCP; TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this ...
    cd04448
    Location:358 → 439
    DEP_PIKfyve; DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol ...
    cd15725
    Location:157 → 218
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins

  8. XM_068223303.1 → XP_068079404.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X8

    UniProtKB/TrEMBL
    A0A8M3B5N9
Nucleotide Protein Strain
Heading Accession and Version

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