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Pikfyve phosphoinositide kinase, FYVE-type zinc finger containing [ Rattus norvegicus (Norway rat) ]

Gene ID: 316457, updated on 13-Apr-2024

Summary

Official Symbol
Pikfyveprovided by RGD
Official Full Name
phosphoinositide kinase, FYVE-type zinc finger containingprovided by RGD
Primary source
RGD:1592067
See related
Ensembl:ENSRNOG00000015158 AllianceGenome:RGD:1592067
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Pip5k3
Summary
Predicted to enable phosphotransferase activity, alcohol group as acceptor and zinc ion binding activity. Predicted to be involved in several processes, including antigen processing and presentation of exogenous peptide antigen via MHC class II; phosphatidylinositol metabolic process; and vesicle organization. Predicted to act upstream of or within myelin assembly. Predicted to be located in several cellular components, including cytoplasmic vesicle membrane; membrane raft; and perinuclear region of cytoplasm. 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, Apr 2022]
Expression
Biased expression in Kidney (RPKM 173.2), Spleen (RPKM 145.9) and 9 other tissues See more
Orthologs
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Genomic context

Location:
9q32
Exon count:
45
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (74057488..74151610)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (66563747..66657873)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (71911744..72005816)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene transfer RNA proline (anticodon AGG) 73 Neighboring gene isocitrate dehydrogenase (NADP(+)) 1 Neighboring gene parathyroid hormone 2 receptor Neighboring gene transcription factor 19, pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables 1-phosphatidylinositol-3-phosphate 5-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables 1-phosphatidylinositol-3-phosphate 5-kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables 1-phosphatidylinositol-4-phosphate 5-kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables 1-phosphatidylinositol-5-kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables 1-phosphatidylinositol-5-kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables protein serine/threonine kinase activity ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II ISO
Inferred from Sequence Orthology
more info
 
involved_in intracellular signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in melanosome organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in melanosome organization ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within myelin assembly ISO
Inferred from Sequence Orthology
more info
 
involved_in neutrophil chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in neutrophil chemotaxis ISO
Inferred from Sequence Orthology
more info
 
NOT involved_in neutrophil degranulation ISO
Inferred from Sequence Orthology
more info
 
involved_in phagosome maturation ISO
Inferred from Sequence Orthology
more info
 
involved_in phagosome-lysosome fusion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in phagosome-lysosome fusion ISO
Inferred from Sequence Orthology
more info
 
involved_in phosphatidylinositol 5-phosphate metabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in protein localization to nucleus ISO
Inferred from Sequence Orthology
more info
 
involved_in protein targeting to membrane ISO
Inferred from Sequence Orthology
more info
 
NOT involved_in receptor-mediated endocytosis ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of autophagosome assembly ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of reactive oxygen species biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in regulation of reactive oxygen species biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in retrograde transport, endosome to Golgi ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in cell-cell junction ISO
Inferred from Sequence Orthology
more info
 
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasmic vesicle ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in early endosome membrane ISO
Inferred from Sequence Orthology
more info
 
located_in endosome membrane ISO
Inferred from Sequence Orthology
more info
 
NOT located_in insulin-responsive compartment ISO
Inferred from Sequence Orthology
more info
 
located_in membrane raft ISO
Inferred from Sequence Orthology
more info
 
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in phagocytic vesicle membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in vesicle membrane ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
1-phosphatidylinositol 3-phosphate 5-kinase
Names
1-phosphatidylinositol-3-phosphate 5-kinase
phosphatidylinositol-3-phosphate 5-kinase type III
phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III
phosphoinositide kinase, FYVE finger containing
NP_001414206.1
XP_006245133.1
XP_006245134.1
XP_006245135.1
XP_006245136.1
XP_006245138.1
XP_006245139.1
XP_006245141.1
XP_038940523.1
XP_038940524.1
XP_038940525.1
XP_063123289.1
XP_063123290.1
XP_063123291.1
XP_063123292.1
XP_063123293.1
XP_063123294.1
XP_063123295.1

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_001427277.1NP_001414206.1  1-phosphatidylinositol 3-phosphate 5-kinase

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000009

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086027.1 Reference GRCr8

    Range
    74057488..74151610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006245076.5XP_006245138.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X4

    See identical proteins and their annotated locations for XP_006245138.1

    UniProtKB/TrEMBL
    A0A8I5ZL06, D3ZYT8
    Related
    ENSRNOP00000078503.1
    Conserved Domains (4) summary
    cd03334
    Location:629889
    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:369450
    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:166227
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:18292095
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins
  2. XM_063267219.1XP_063123289.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X5

  3. XM_063267220.1XP_063123290.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X7

  4. XM_063267222.1XP_063123292.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X10

  5. XM_006245077.5XP_006245139.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X4

    See identical proteins and their annotated locations for XP_006245139.1

    UniProtKB/TrEMBL
    A0A8I5ZL06, D3ZYT8
    Related
    ENSRNOP00000020447.6
    Conserved Domains (4) summary
    cd03334
    Location:629889
    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:369450
    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:166227
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:18292095
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins
  6. XM_006245074.5XP_006245136.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X4

    See identical proteins and their annotated locations for XP_006245136.1

    UniProtKB/TrEMBL
    A0A8I5ZL06, D3ZYT8
    Conserved Domains (4) summary
    cd03334
    Location:629889
    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:369450
    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:166227
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:18292095
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins
  7. XM_039084595.2XP_038940523.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X4

    UniProtKB/TrEMBL
    A0A8I5ZL06, D3ZYT8
    Conserved Domains (4) summary
    cd03334
    Location:629889
    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:369450
    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:166227
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:18292095
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins
  8. XM_006245071.3XP_006245133.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X1

    See identical proteins and their annotated locations for XP_006245133.1

    UniProtKB/TrEMBL
    A0A8I5YBG1, A0A8I5ZL06
    Related
    ENSRNOP00000076715.1
    Conserved Domains (5) summary
    cd00139
    Location:18032116
    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:649909
    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:389470
    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:186247
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cl12013
    Location:14301477
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  9. XM_039084596.2XP_038940524.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X6

    UniProtKB/TrEMBL
    A0A8I5ZL06
    Conserved Domains (4) summary
    cd03334
    Location:649909
    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:389470
    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:186247
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cd17300
    Location:18212087
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins
  10. XM_006245072.3XP_006245134.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X2

    See identical proteins and their annotated locations for XP_006245134.1

    UniProtKB/TrEMBL
    A0A8I5ZL06
    Conserved Domains (5) summary
    cd00139
    Location:18022115
    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:648908
    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:388469
    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:185246
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cl12013
    Location:14291476
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  11. XM_006245079.3XP_006245141.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X8

    See identical proteins and their annotated locations for XP_006245141.1

    UniProtKB/TrEMBL
    A6IPK0
    Related
    ENSRNOP00000088892.1
    Conserved Domains (5) summary
    cd00139
    Location:17462059
    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:592852
    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:388469
    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:185246
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cl12013
    Location:13731420
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  12. XM_006245073.3XP_006245135.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X3

    See identical proteins and their annotated locations for XP_006245135.1

    UniProtKB/TrEMBL
    A0A8I5ZL06
    Conserved Domains (5) summary
    cd00139
    Location:17912104
    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:637897
    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:377458
    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:174235
    FYVE_PIKfyve_Fab1; FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins
    cl12013
    Location:14181465
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  13. XM_063267221.1XP_063123291.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X9

    UniProtKB/TrEMBL
    A0A8I6AAS9
  14. XM_063267223.1XP_063123293.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X11

  15. XM_063267224.1XP_063123294.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X13

  16. XM_063267225.1XP_063123295.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X14

  17. XM_039084597.2XP_038940525.1  1-phosphatidylinositol 3-phosphate 5-kinase isoform X12

    Conserved Domains (2) summary
    cd17300
    Location:10321298
    PIPKc_PIKfyve; Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins
    cl02777
    Location:192
    chaperonin_like; chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I ...