Pik3c2b phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pik3c2bprovided by RGD
Official Full Name: phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 betaprovided by RGD
Primary source: RGD:1306541
See related: EnsemblRapid:ENSRNOG00000029938 AllianceGenome:RGD:1306541
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable 1-phosphatidylinositol-3-kinase activity and 1-phosphatidylinositol-4-phosphate 3-kinase activity. Predicted to be involved in cell migration; intracellular signal transduction; and phosphatidylinositol-3-phosphate biosynthetic process. Predicted to act upstream of or within autophagosome organization and cellular response to starvation. Predicted to be located in cytosol; endocytic vesicle; and nucleoplasm. Predicted to be active in cytoplasm and plasma membrane. Orthologous to human PIK3C2B (phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Heart (RPKM 69.9), Muscle (RPKM 58.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 35

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (47046866..47107733)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (44494673..44555663)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (49848939..49909404)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Missense single-nucleotide polymorphism in the Pik3c2b gene associated with autophagy regulation in in the progression of Age-related macular degeneration was found.
Title: Involvement of the autophagic pathway in the progression of AMD-like retinopathy in senescence-accelerated OXYS rats.
Activated during compensatory liver growth, which clearly demonstrates that different class II PI3K enzymes have different subnuclear localization.
Title: Activation of phosphoinositide 3-kinase C2 beta in the nuclear matrix during compensatory liver growth.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 1-phosphatidylinositol-3-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 1-phosphatidylinositol-3-kinase activity	ISO Inferred from Sequence Orthology more info
enables 1-phosphatidylinositol-4-phosphate 3-kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 1-phosphatidylinositol-4-phosphate 3-kinase activity	ISO Inferred from Sequence Orthology more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables lipid kinase activity	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within autophagosome organization	ISO Inferred from Sequence Orthology more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cellular response to starvation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within macroautophagy	ISO Inferred from Sequence Orthology more info
involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
involved_in phosphatidylinositol-3-phosphate biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within phosphatidylinositol-3-phosphate biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in phosphatidylinositol-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta

Names: nuclear cap binding protein subunit 2; phosphoinositide-3-kinase, class 2, beta polypeptide

NP_001099421.1

EC 2.7.1.154

XP_006249816.1

EC 2.7.1.154

XP_006249818.1

EC 2.7.1.154

XP_063128143.1

EC 2.7.1.154

XP_063128144.1

EC 2.7.1.154

XP_063128145.1

EC 2.7.1.154

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_001105951.1 → NP_001099421.1 phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta

See identical proteins and their annotated locations for NP_001099421.1

Status: PROVISIONAL

Source sequence(s)

CH473958

UniProtKB/TrEMBL

A6IC68, D3ZVF3

Related

ENSRNOP00000051488.3, ENSRNOT00000042125.6

Conserved Domains (7) summary

cd00895
Location:974 → 1327

PI3Kc_C2_beta; Catalytic domain of Class II Phosphoinositide 3-kinase beta

cd07290
Location:1356 → 1464

PX_PI3K_C2_beta; The phosphoinositide binding Phox Homology Domain of the Beta Isoform of Class II Phosphoinositide 3-Kinases

cd04012
Location:609 → 781

C2A_PI3K_class_II; C2 domain first repeat present in class II phosphatidylinositol 3-kinases (PI3Ks)

cd08381
Location:1492 → 1614

C2B_PI3K_class_II; C2 domain second repeat present in class II phosphatidylinositol 3-kinases (PI3Ks)

cd00869
Location:800 → 968

PI3Ka_II; Phosphoinositide 3-kinase (PI3K) class II, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, class II PI3-kinases ...

pfam00794
Location:363 → 465

PI3K_rbd; PI3-kinase family, ras-binding domain

pfam13646
Location:882 → 965

HEAT_2; HEAT repeats

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

NC_086031.1 Reference GRCr8

Range

47046866..47107733

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272074.1 → XP_063128144.1 phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta isoform X1
XM_063272075.1 → XP_063128145.1 phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta isoform X3
XM_063272073.1 → XP_063128143.1 phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta isoform X1
XM_006249754.5 → XP_006249816.1 phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta isoform X2

See identical proteins and their annotated locations for XP_006249816.1

UniProtKB/TrEMBL

A0A0G2K1Q0

Related

ENSRNOP00000071933.2, ENSRNOT00000090170.3

Conserved Domains (6) summary

cd00895
Location:986 → 1339

PI3Kc_C2_beta; Catalytic domain of Class II Phosphoinositide 3-kinase beta

cd07290
Location:1368 → 1476

PX_PI3K_C2_beta; The phosphoinositide binding Phox Homology Domain of the Beta Isoform of Class II Phosphoinositide 3-Kinases

cd04012
Location:621 → 793

C2A_PI3K_class_II; C2 domain first repeat present in class II phosphatidylinositol 3-kinases (PI3Ks)

cd08381
Location:1504 → 1626

C2B_PI3K_class_II; C2 domain second repeat present in class II phosphatidylinositol 3-kinases (PI3Ks)

cd00869
Location:812 → 980

PI3Ka_II; Phosphoinositide 3-kinase (PI3K) class II, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, class II PI3-kinases ...

pfam00794
Location:363 → 465

PI3K_rbd; PI3-kinase family, ras-binding domain
XM_006249756.5 → XP_006249818.1 phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit beta isoform X4

UniProtKB/TrEMBL

A0A0G2K1Q0

Conserved Domains (7) summary

cd00895
Location:765 → 1118

PI3Kc_C2_beta; Catalytic domain of Class II Phosphoinositide 3-kinase beta

cd07290
Location:1147 → 1255

PX_PI3K_C2_beta; The phosphoinositide binding Phox Homology Domain of the Beta Isoform of Class II Phosphoinositide 3-Kinases

cd04012
Location:400 → 572

C2A_PI3K_class_II; C2 domain first repeat present in class II phosphatidylinositol 3-kinases (PI3Ks)

cd08381
Location:1283 → 1405

C2B_PI3K_class_II; C2 domain second repeat present in class II phosphatidylinositol 3-kinases (PI3Ks)

cd00869
Location:591 → 759

PI3Ka_II; Phosphoinositide 3-kinase (PI3K) class II, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, class II PI3-kinases ...

pfam00794
Location:142 → 244

PI3K_rbd; PI3-kinase family, ras-binding domain

pfam13646
Location:673 → 756

HEAT_2; HEAT repeats