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

Summary

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 and 1-phosphatidylinositol-5-kinase 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

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_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Disruption of PIKFYVE causes congenital cataract in human and zebrafish.
Title: Disruption of PIKFYVE causes congenital cataract in human and zebrafish.
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.

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General gene information

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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

EC 2.7.1.68

XP_005167723.1

EC 2.7.1.68

XP_005167724.1

EC 2.7.1.68

XP_005167726.1

EC 2.7.1.68

XP_005167727.1

EC 2.7.1.68

XP_009302997.1

EC 2.7.1.68

XP_068079402.1

EC 2.7.1.68

XP_068079403.1

EC 2.7.1.68

XP_068079404.1

EC 2.7.1.68

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)

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

NC_007120.7 Reference GRCz11 Primary Assembly

Range

32073673..32104183

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8M3AW23
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
XM_068223302.1 → XP_068079403.1 1-phosphatidylinositol 3-phosphate 5-kinase isoform X3

UniProtKB/TrEMBL

A0A8M3B5N9
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
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
XM_068223303.1 → XP_068079404.1 1-phosphatidylinositol 3-phosphate 5-kinase isoform X8

UniProtKB/TrEMBL

A0A8M3B5N9