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:CRB2

Protein Summary

Gene summary

Gene name: CRB2
ASpdb.0 ID: 286204
	Gene
Gene symbol	CRB2
Gene ID	286204
Gene name	crumbs cell polarity complex component 2
Synonyms	FSGS9\|VMCKD
Cytomap	9q33.3
Type of gene	protein-coding
Description	protein crumbs homolog 2crumbs 2, cell polarity complex componentcrumbs family member 2crumbs-like protein 2
Modification date	20240416
UniProtAcc	Q5IJ48

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CRB2	GO:0032991	protein-containing complex	20299451

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
Q5IJ48-1	Q5IJ48-1_2wo6_C.pdb	2WO6	X-ray	2.5	C	4	9

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

Q5IJ48

CRB2

Q5IJ48-1

Q5IJ48-2

1285

1176

1131

1176

Substitution

LPVPSKECSLNVTCLDGSPCEGGSPAANCSCLEGLAGQRCQVPTLP

WDGWAGGWAANAPWGYGGAEKSARSVDESLPFPGPHVLICDMRRTV

1131

1176

Q5IJ48

CRB2

Q5IJ48-1

Q5IJ48-2

1285

1176

1177

1285

Deletion

none

1176

Q5IJ48

CRB2

Q5IJ48-1

Q5IJ48-3

1285

953

332

Deletion

none

Q5IJ48

CRB2

Q5IJ48-1

Q5IJ48-3

1285

953

333

351

Substitution

GHCQDLPNGFQCHCPDGYA

MAMEPGALWTFLGHLWLLA

Multiple sequence alignment of our canonical and alternatively spliced CRB2

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CRB2

UniProt-id	ENSG	ENST	ENSP
Q5IJ48-1	ENSG00000148204.12	ENST00000373631.8	ENSP00000362734.3
Q5IJ48-2	ENSG00000148204.12	ENST00000359999.7	ENSP00000353092.3
Q5IJ48-3	ENSG00000148204.12	ENST00000460253.1	ENSP00000435279.1

UniProt-id	NM ID	NP ID
Q5IJ48-1	NM_173689.6	NP_775960.4
Q5IJ48-3	XM_005251934.2	XP_005251991.1

Amino acid sequences of our canonical and alternatively spliced CRB2

accession_id	Protein sequence
Q5IJ48-1	MALARPGTPDPQALASVLLLLLWAPALSLLAGTVPSEPPSACASDPCAPGTECQATESGGYTCGPMEPRGCATQPCHHGALCVPQGPDPT GFRCYCVPGFQGPRCELDIDECASRPCHHGATCRNLADRYECHCPLGYAGVTCEMEVDECASAPCLHGGSCLDGVGSFRCVCAPGYGGTR CQLDLDECQSQPCAHGGTCHDLVNGFRCDCAGTGYEGTHCEREVLECASAPCEHNASCLEGLGSFRCLCWPGYSGELCEVDEDECASSPC QHGGRCLQRSDPALYGGVQAAFPGAFSFRHAAGFLCHCPPGFEGADCGVEVDECASRPCLNGGHCQDLPNGFQCHCPDGYAGPTCEEDVD ECLSDPCLHGGTCSDTVAGYICRCPETWGGRDCSVQLTGCQGHTCPLAATCIPIFESGVHSYVCHCPPGTHGPFCGQNTTFSVMAGSPIQ ASVPAGGPLGLALRFRTTLPAGTLATRNDTKESLELALVAATLQATLWSYSTTVLVLRLPDLALNDGHWHQVEVVLHLATLELRLWHEGC PARLCVASGPVALASTASATPLPAGISSAQLGDATFAGCLQDVRVDGHLLLPEDLGENVLLGCERREQCRPLPCVHGGSCVDLWTHFRCD CARPHRGPTCADEIPAATFGLGGAPSSASFLLQELPGPNLTVSFLLRTRESAGLLLQFANDSAAGLTVFLSEGRIRAEVPGSPAVVLPGR WDDGLRHLVMLSFGPDQLQDLGQHVHVGGRLLAADSQPWGGPFRGCLQDLRLDGCHLPFFPLPLDNSSQPSELGGRQSWNLTAGCVSEDM CSPDPCFNGGTCLVTWNDFHCTCPANFTGPTCAQQLWCPGQPCLPPATCEEVPDGFVCVAEATFREGPPAAFSGHNASSGRLLGGLSLAF RTRDSEAWLLRAAAGALEGVWLAVRNGSLAGGVRGGHGLPGAVLPIPGPRVADGAWHRVRLAMERPAATTSRWLLWLDGAATPVALRGLA SDLGFLQGPGAVRILLAENFTGCLGRVALGGLPLPLARPRPGAAPGAREHFASWPGTPAPILGCRGAPVCAPSPCLHDGACRDLFDAFAC ACGPGWEGPRCEAHVDPCHSAPCARGRCHTHPDGRFECRCPPGFGGPRCRLPVPSKECSLNVTCLDGSPCEGGSPAANCSCLEGLAGQRC QVPTLPCEANPCLNGGTCRAAGGVSECICNARFSGQFCEVAKGLPLPLPFPLLEVAVPAACACLLLLLLGLLSGILAARKRRQSEGTYSP
Q5IJ48-2	MALARPGTPDPQALASVLLLLLWAPALSLLAGTVPSEPPSACASDPCAPGTECQATESGGYTCGPMEPRGCATQPCHHGALCVPQGPDPT GFRCYCVPGFQGPRCELDIDECASRPCHHGATCRNLADRYECHCPLGYAGVTCEMEVDECASAPCLHGGSCLDGVGSFRCVCAPGYGGTR CQLDLDECQSQPCAHGGTCHDLVNGFRCDCAGTGYEGTHCEREVLECASAPCEHNASCLEGLGSFRCLCWPGYSGELCEVDEDECASSPC QHGGRCLQRSDPALYGGVQAAFPGAFSFRHAAGFLCHCPPGFEGADCGVEVDECASRPCLNGGHCQDLPNGFQCHCPDGYAGPTCEEDVD ECLSDPCLHGGTCSDTVAGYICRCPETWGGRDCSVQLTGCQGHTCPLAATCIPIFESGVHSYVCHCPPGTHGPFCGQNTTFSVMAGSPIQ ASVPAGGPLGLALRFRTTLPAGTLATRNDTKESLELALVAATLQATLWSYSTTVLVLRLPDLALNDGHWHQVEVVLHLATLELRLWHEGC PARLCVASGPVALASTASATPLPAGISSAQLGDATFAGCLQDVRVDGHLLLPEDLGENVLLGCERREQCRPLPCVHGGSCVDLWTHFRCD CARPHRGPTCADEIPAATFGLGGAPSSASFLLQELPGPNLTVSFLLRTRESAGLLLQFANDSAAGLTVFLSEGRIRAEVPGSPAVVLPGR WDDGLRHLVMLSFGPDQLQDLGQHVHVGGRLLAADSQPWGGPFRGCLQDLRLDGCHLPFFPLPLDNSSQPSELGGRQSWNLTAGCVSEDM CSPDPCFNGGTCLVTWNDFHCTCPANFTGPTCAQQLWCPGQPCLPPATCEEVPDGFVCVAEATFREGPPAAFSGHNASSGRLLGGLSLAF RTRDSEAWLLRAAAGALEGVWLAVRNGSLAGGVRGGHGLPGAVLPIPGPRVADGAWHRVRLAMERPAATTSRWLLWLDGAATPVALRGLA SDLGFLQGPGAVRILLAENFTGCLGRVALGGLPLPLARPRPGAAPGAREHFASWPGTPAPILGCRGAPVCAPSPCLHDGACRDLFDAFAC ACGPGWEGPRCEAHVDPCHSAPCARGRCHTHPDGRFECRCPPGFGGPRCRWDGWAGGWAANAPWGYGGAEKSARSVDESLPFPGPHVLIC
Q5IJ48-3	MAMEPGALWTFLGHLWLLAGPTCEEDVDECLSDPCLHGGTCSDTVAGYICRCPETWGGRDCSVQLTGCQGHTCPLAATCIPIFESGVHSY VCHCPPGTHGPFCGQNTTFSVMAGSPIQASVPAGGPLGLALRFRTTLPAGTLATRNDTKESLELALVAATLQATLWSYSTTVLVLRLPDL ALNDGHWHQVEVVLHLATLELRLWHEGCPARLCVASGPVALASTASATPLPAGISSAQLGDATFAGCLQDVRVDGHLLLPEDLGENVLLG CERREQCRPLPCVHGGSCVDLWTHFRCDCARPHRGPTCADEIPAATFGLGGAPSSASFLLQELPGPNLTVSFLLRTRESAGLLLQFANDS AAGLTVFLSEGRIRAEVPGSPAVVLPGRWDDGLRHLVMLSFGPDQLQDLGQHVHVGGRLLAADSQPWGGPFRGCLQDLRLDGCHLPFFPL PLDNSSQPSELGGRQSWNLTAGCVSEDMCSPDPCFNGGTCLVTWNDFHCTCPANFTGPTCAQQLWCPGQPCLPPATCEEVPDGFVCVAEA TFREGPPAAFSGHNASSGRLLGGLSLAFRTRDSEAWLLRAAAGALEGVWLAVRNGSLAGGVRGGHGLPGAVLPIPGPRVADGAWHRVRLA MERPAATTSRWLLWLDGAATPVALRGLASDLGFLQGPGAVRILLAENFTGCLGRVALGGLPLPLARPRPGAAPGAREHFASWPGTPAPIL GCRGAPVCAPSPCLHDGACRDLFDAFACACGPGWEGPRCEAHVDPCHSAPCARGRCHTHPDGRFECRCPPGFGGPRCRLPVPSKECSLNV TCLDGSPCEGGSPAANCSCLEGLAGQRCQVPTLPCEANPCLNGGTCRAAGGVSECICNARFSGQFCEVAKGLPLPLPFPLLEVAVPAACA

Protein Functional Features

Main function of this protein. (from UniProt)

CRB2 (go to UniProt):Q5IJ48

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
Q5IJ48	Transmembrane	1225	1245	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=1177;End=1285
Q5IJ48	Domain	67	106	Note=EGF-like 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	108	144	Note=EGF-like 2%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	146	182	Note=EGF-like 3%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	184	221	Note=EGF-like 4%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	223	259	Note=EGF-like 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	261	318	Note=EGF-like 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	320	356	Note=EGF-like 7%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1;End=332
Q5IJ48	Domain	320	356	Note=EGF-like 7%3B calcium-binding;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Substitution;Start=333;End=351
Q5IJ48	Domain	1134	1171	Note=EGF-like 14;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Substitution;Start=1131;End=1176
Q5IJ48	Domain	1173	1209	Note=EGF-like 15;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Substitution;Start=1131;End=1176
Q5IJ48	Domain	1173	1209	Note=EGF-like 15;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00076	Type=Deletion;Start=1177;End=1285
Q5IJ48	Region	1	350	Note=Required for maximum inhibition of APP amyloid-beta peptide secretion;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20299451;Dbxref=PMID:20299451	Type=Deletion;Start=1;End=332
Q5IJ48	Region	1	350	Note=Required for maximum inhibition of APP amyloid-beta peptide secretion;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:20299451;Dbxref=PMID:20299451	Type=Substitution;Start=333;End=351
Q5IJ48	Region	1249	1285	Note=Interaction with EPB41L5;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17920587;Dbxref=PMID:17920587	Type=Deletion;Start=1177;End=1285

Gene Isoform Structures and Expression Levels for CRB2

Gene structures of our canonical and alternative spliced genes of CRB2
* 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 Q5IJ48-1

3D view using mol* of Q5IJ48-2

3D view using mol* of Q5IJ48-3

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 Q5IJ48-1

pLDDT distribution across the protein length of Q5IJ48-2

pLDDT distribution across the protein length of Q5IJ48-3

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 Q5IJ48-1

Ramachandran plot of Q5IJ48-2

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
Q5IJ48-1	1.013	107	1.009	246.96	0.552	0.717	0.945	0.604	1.11	0.544	0.852	865,866,867,868,880,882,1025,1026,1027,1028,1029,1 035,1036,1037,1040,1041,1042,1043,1044,1046,1047,1 048,1049,1050,1052
Q5IJ48-2	0.949	172	0.968	451.388	0.553	0.622	0.833	0.435	1.058	0.411	1.215	636,637,642,660,661,662,664,665,666,772,773,775,77 6,777,778,781,782,783,784,785,787,788,789,790,791, 792,793,794,795,796
Q5IJ48-3	0.919	89	0.939	376.271	0.703	0.623	0.838	0.573	0.986	0.581	1.177	304,328,330,331,332,333,334,440,441,443,445,446,44 9,450,451,452,453,454,455,457,458,459,460,461,462, 463,464

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 Q5IJ48-1_Q5IJ48-1_2wo6_C.pdb

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

3D view using mol* of Q5IJ48-1_2wo6_C_Q5IJ48-2.pdb

3D view using mol* of Q5IJ48-1_2wo6_C_Q5IJ48-3.pdb

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

3D view using mol* of Q5IJ48-1_Q5IJ48-2.pdb

3D view using mol* of Q5IJ48-1_Q5IJ48-3.pdb

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

./stats/secondary_structure/figure/Q5IJ48-1_vs_Q5IJ48-2.png

./stats/secondary_structure/figure/Q5IJ48-1_vs_Q5IJ48-3.png

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

./stats/relative_asa/Q5IJ48-1_vs_Q5IJ48-2.png

./stats/relative_asa/Q5IJ48-1_vs_Q5IJ48-3.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q5IJ48	Region	1249	1285	Note=Interaction with EPB41L5;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17920587;Dbxref=PMID:17920587	Type=Deletion;Start=1177;End=1285

Interactors from STRING.

Gene name

Interactors

Related Drugs to CRB2

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to CRB2

Previous studies relating to the alternative splicing of CRB2 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CRB2

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance