ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:PIK3R1

Protein Summary

Gene summary

Gene name: PIK3R1
ASpdb.0 ID: 5295
	Gene
Gene symbol	PIK3R1
Gene ID	5295
Gene name	phosphoinositide-3-kinase regulatory subunit 1
Synonyms	AGM7\|GRB1\|IMD36\|p85\|p85-ALPHA\|p85alpha
Cytomap	5q13.1
Type of gene	protein-coding
Description	phosphatidylinositol 3-kinase regulatory subunit alphaPI3 kinase-associated p85PI3-kinase subunit p85-alphaPI3K regulatory subunit alphagrowth factor receptor bound 1phosphatidylinositol 3-kinase 85 kDa regulatory subunit alphaphosphatidylinositol 3
Modification date	20240403
UniProtAcc	P27986

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	PIK3R1	GO:0005737	cytoplasm	20348923
Gene	PIK3R1	GO:0034143	regulation of toll-like receptor 4 signaling pathway	19289601
Gene	PIK3R1	GO:0034976	response to endoplasmic reticulum stress	20348923
Gene	PIK3R1	GO:0042307	positive regulation of protein import into nucleus	20348923
Gene	PIK3R1	GO:0043125	ErbB-3 class receptor binding	10572067
Gene	PIK3R1	GO:0043491	phosphatidylinositol 3-kinase/protein kinase B signal transduction	7782332
Gene	PIK3R1	GO:0043559	insulin binding	8440175
Gene	PIK3R1	GO:0048009	insulin-like growth factor receptor signaling pathway	7782332
Gene	PIK3R1	GO:0050821	protein stabilization	20348923
Gene	PIK3R1	GO:0060396	growth hormone receptor signaling pathway	7782332

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
P27986-1	P27986-1_4ykn_A.pdb	4YKN	X-ray	2.9	A	323	615

ASpdb's canonical and alternatively spliced isoform information.

accession_id

gene_name

canonical_id

alternative_id

canonical_length

alternative_length

canonical_start

canonical_end

type

originalSEQ

variationSEQ

alternative_start

alternative_end

P27986

PIK3R1

P27986-1

P27986-2

724

454

270

Deletion

none

P27986

PIK3R1

P27986-1

P27986-2

724

454

271

304

Substitution

MLFRFSAASSDNTENLIKVIEILISTEWNERQPA

MYNTVWNMEDLDLEYAKTDINCGTDLMFYIEMDP

P27986

PIK3R1

P27986-1

P27986-3

724

424

300

Deletion

none

P27986

PIK3R1

P27986-1

P27986-3

724

424

301

306

Substitution

RQPAPA

MHNLQT

P27986

PIK3R1

P27986-1

P27986-4

724

732

605

Substitution

ENFLSCLPS

605

613

P27986

PIK3R1

P27986-1

P27986-5

724

361

363

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced PIK3R1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PIK3R1

UniProt-id	ENSG	ENST	ENSP
P27986-1	ENSG00000145675.16	ENST00000517643.2	ENSP00000513333.1
P27986-1	ENSG00000145675.16	ENST00000521381.6	ENSP00000428056.1
P27986-1	ENSG00000145675.16	ENST00000521657.6	ENSP00000429277.1
P27986-1	ENSG00000145675.16	ENST00000697458.1	ENSP00000513316.1
P27986-2	ENSG00000145675.16	ENST00000336483.10	ENSP00000338554.5
P27986-3	ENSG00000145675.16	ENST00000320694.13	ENSP00000323512.8
P27986-4	ENSG00000145675.16	ENST00000697461.1	ENSP00000513319.1
P27986-5	ENSG00000145675.16	ENST00000523872.1	ENSP00000430098.1
P27986-5	ENSG00000145675.16	ENST00000697467.1	ENSP00000513325.1

UniProt-id	NM ID	NP ID
P27986-1	NM_181523.2	NP_852664.1
P27986-1	XM_005248542.3	XP_005248599.1
P27986-1	XM_017009585.1	XP_016865074.1
P27986-2	NM_181504.3	NP_852556.2
P27986-3	NM_181524.1	NP_852665.1
P27986-5	NM_001242466.1	NP_001229395.1

Amino acid sequences of our canonical and alternatively spliced PIK3R1

accession_id	Protein sequence
P27986-1	MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIGWLNGYNETTGERGDFPGTYVEYIGRKKISPPTPKPR PPRPLPVAPGSSKTEADVEQQALTLPDLAEQFAPPDIAPPLLIKLVEAIEKKGLECSTLYRTQSSSNLAELRQLLDCDTPSVDLEMIDVH VLADAFKRYLLDLPNPVIPAAVYSEMISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTLQYLLKHFFKLSQTSSKNLLNARVLSEIFSP MLFRFSAASSDNTENLIKVIEILISTEWNERQPAPALPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDA STKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLH EYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIID SRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGNENTEDQYSLVEDDEDLPHHDEKTWNVGSSN RNKAENLLRGKRDGTFLVRESSKQGCYACSVVVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNVTLAYPVYA
P27986-2	MYNTVWNMEDLDLEYAKTDINCGTDLMFYIEMDPPALPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDA STKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLH EYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIID SRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGNENTEDQYSLVEDDEDLPHHDEKTWNVGSSN RNKAENLLRGKRDGTFLVRESSKQGCYACSVVVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNVTLAYPVYA
P27986-3	MHNLQTLPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKY GFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMK RTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDL IQLRKTRDQYLMWLTQKGVRQKKLNEWLGNENTEDQYSLVEDDEDLPHHDEKTWNVGSSNRNKAENLLRGKRDGTFLVRESSKQGCYACS
P27986-4	MSAEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIGWLNGYNETTGERGDFPGTYVEYIGRKKISPPTPKPR PPRPLPVAPGSSKTEADVEQQALTLPDLAEQFAPPDIAPPLLIKLVEAIEKKGLECSTLYRTQSSSNLAELRQLLDCDTPSVDLEMIDVH VLADAFKRYLLDLPNPVIPAAVYSEMISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTLQYLLKHFFKLSQTSSKNLLNARVLSEIFSP MLFRFSAASSDNTENLIKVIEILISTEWNERQPAPALPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDA STKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLH EYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIID SRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGNENTEENFLSCLPSQYSLVEDDEDLPHHDEK TWNVGSSNRNKAENLLRGKRDGTFLVRESSKQGCYACSVVVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNV
P27986-5	MHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYN TQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRR RLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGNENTEDQYSLVEDDEDLPHHDEKTWNVGSSNRNK AENLLRGKRDGTFLVRESSKQGCYACSVVVDGEVKHCVINKTATGYGFAEPYNLYSSLKELVLHYQHTSLVQHNDSLNVTLAYPVYAQQR

Protein Functional Features

Main function of this protein. (from UniProt)

PIK3R1 (go to UniProt):P27986

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
P27986	Domain	3	79	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192	Type=Deletion;Start=1;End=270
P27986	Domain	3	79	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192	Type=Deletion;Start=1;End=300
P27986	Domain	3	79	Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00192	Type=Deletion;Start=1;End=363
P27986	Domain	113	301	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Deletion;Start=1;End=270
P27986	Domain	113	301	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Substitution;Start=271;End=304
P27986	Domain	113	301	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Deletion;Start=1;End=300
P27986	Domain	113	301	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Substitution;Start=301;End=306
P27986	Domain	113	301	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Deletion;Start=1;End=363
P27986	Domain	333	428	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191	Type=Deletion;Start=1;End=363
P27986	Region	80	108	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=270
P27986	Region	80	108	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=300
P27986	Region	80	108	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=363
P27986	Compositional bias	84	98	Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=270
P27986	Compositional bias	84	98	Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=300
P27986	Compositional bias	84	98	Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=363

Gene Isoform Structures and Expression Levels for PIK3R1

Gene structures of our canonical and alternative spliced genes of PIK3R1
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of P27986-1

3D view using mol* of P27986-2

3D view using mol* of P27986-3

3D view using mol* of P27986-4

3D view using mol* of P27986-5

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of P27986-1

pLDDT distribution across the protein length of P27986-2

pLDDT distribution across the protein length of P27986-3

pLDDT distribution across the protein length of P27986-4

pLDDT distribution across the protein length of P27986-5

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of P27986-1

Ramachandran plot of P27986-3

Ramachandran plot of P27986-4

Ramachandran plot of P27986-5

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
P27986-1	1.029	102	1.069	427.035	0.595	0.698	0.876	0.674	0.89	0.757	0.868	307,308,335,342,345,346,348,350,351,354,426,427,42 8,429,432,433,571,574,575,578,579,582
P27986-2	1.052	142	1.116	755.286	0.626	0.681	0.901	0.925	0.714	1.296	1.294	28,30,32,34,35,37,65,68,72,75,76,78,79,158,159,160 ,162,186,190,193,194,197,198,297,300,301,304,305,3 08,309,311,312,315,316
P27986-3	1.014	92	1.062	446.929	0.643	0.685	0.898	0.907	0.77	1.178	1.462	35,38,42,45,46,48,49,128,130,132,156,270,271,274,2 75,278,279,281,282,286
P27986-4	1.018	203	1.059	738.822	0.57	0.68	0.902	0.69	0.888	0.776	1.316	304,305,306,307,308,309,310,311,335,338,342,345,34 6,348,349,350,351,354,426,427,428,429,430,431,432, 433,435,570,571,574,575,578,579,581,582,586
P27986-5	0.916	77	0.925	150.234	0.45	0.679	1.001	1.099	0.944	1.165	0.396	7,8,9,10,42,46,59,60,61,62,63,64,65

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of P27986-1_P27986-1_4ykn_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P27986-1_4ykn_A_P27986-2.pdb

3D view using mol* of P27986-1_4ykn_A_P27986-3.pdb

3D view using mol* of P27986-1_4ykn_A_P27986-4.pdb

3D view using mol* of P27986-1_4ykn_A_P27986-5.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P27986-1_P27986-2.pdb

3D view using mol* of P27986-1_P27986-3.pdb

3D view using mol* of P27986-1_P27986-4.pdb

3D view using mol* of P27986-1_P27986-5.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/P27986-1_vs_P27986-2.png

./stats/secondary_structure/figure/P27986-1_vs_P27986-3.png

./stats/secondary_structure/figure/P27986-1_vs_P27986-4.png

./stats/secondary_structure/figure/P27986-1_vs_P27986-5.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/P27986-1_vs_P27986-2.png

./stats/relative_asa/P27986-1_vs_P27986-3.png

./stats/relative_asa/P27986-1_vs_P27986-4.png

./stats/relative_asa/P27986-1_vs_P27986-5.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to PIK3R1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P27986	PIK3R1	DB05210	SF1126	investigational
P27986	PIK3R1	DB08059	Wortmannin	experimental
P27986	PIK3R1	DB06486	Enzastaurin	investigational

Related Diseases to PIK3R1

Previous studies relating to the alternative splicing of PIK3R1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in PIK3R1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance