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:CD22

Protein Summary

Gene summary

Gene name: CD22
ASpdb.0 ID: 933
	Gene
Gene symbol	CD22
Gene ID	933
Gene name	CD22 molecule
Synonyms	SIGLEC-2\|SIGLEC2
Cytomap	19q13.12
Type of gene	protein-coding
Description	B-cell receptor CD22B-lymphocyte cell adhesion moleculeBL-CAMCD22 antigenT-cell surface antigen Leu-14sialic acid-binding Ig-like lectin 2
Modification date	20240305
UniProtAcc	P20273

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CD22	GO:0005769	early endosome	17562860
Gene	CD22	GO:0030100	regulation of endocytosis	17562860
Gene	CD22	GO:0042113	B cell activation	26017478
Gene	CD22	GO:0050859	negative regulation of B cell receptor signaling pathway	26017478
Gene	CD22	GO:0055037	recycling endosome	17562860

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
P20273-1	P20273-1_5vkj_A.pdb	5VKJ	X-ray	2.12	A	20	328

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

P20273

CD22

P20273-1

P20273-2

847

670

241

417

Deletion

none

240

P20273

CD22

P20273-1

P20273-3

847

759

330

417

Deletion

none

329

P20273

CD22

P20273-1

P20273-4

847

751

737

751

Substitution

VRRAPLSEGPHSLGC

RCRVLRDAETSPGLR

737

751

P20273

CD22

P20273-1

P20273-4

847

751

752

847

Deletion

none

751

P20273

CD22

P20273-1

P20273-5

847

675

Substitution

MHL

MSL

P20273

CD22

P20273-1

P20273-5

847

675

175

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced CD22

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CD22

UniProt-id	ENSG	ENST	ENSP
P20273-1	ENSG00000012124.17	ENST00000085219.10	ENSP00000085219.4
P20273-2	ENSG00000012124.17	ENST00000341773.10	ENSP00000339349.6
P20273-2	ENSG00000012124.17	ENST00000594250.5	ENSP00000469984.1
P20273-3	ENSG00000012124.17	ENST00000536635.6	ENSP00000442279.1
P20273-4	ENSG00000012124.17	ENST00000544992.6	ENSP00000441237.1
P20273-5	ENSG00000012124.17	ENST00000419549.6	ENSP00000403822.2

UniProt-id	NM ID	NP ID
P20273-1	NM_001771.3	NP_001762.2
P20273-2	NM_001185101.1	NP_001172030.1
P20273-3	NM_001185099.1	NP_001172028.1
P20273-4	NM_001185100.1	NP_001172029.1
P20273-5	NM_001278417.1	NP_001265346.1

Amino acid sequences of our canonical and alternatively spliced CD22

accession_id	Protein sequence
P20273-1	MHLLGPWLLLLVLEYLAFSDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKNTSKFDGTRLYESTKDGKVPSEQK RVQFLGDKNKNCTLSIHPVHLNDSGQLGLRMESKTEKWMERIHLNVSERPFPPHIQLPPEIQESQEVTLTCLLNFSCYGYPIQLQWLLEG VPMRQAAVTSTSLTIKSVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSNDTVQLNVKHTPKLEIKVTPSDAIVREGDSVTMTCEVSSS NPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVGPGRSEEVFLQVQYAPEPSTVQILHSPAVEGSQVEFLCMSLANPL PTNYTWYHNGKEMQGRTEEKVHIPKILPWHAGTYSCVAENILGTGQRGPGAELDVQYPPKKVTTVIQNPMPIREGDTVTLSCNYNSSNPS VTRYEWKPHGAWEEPSLGVLKIQNVGWDNTTIACAACNSWCSWASPVALNVQYAPRDVRVRKIKPLSEIHSGNSVSLQCDFSSSHPKEVQ FFWEKNGRLLGKESQLNFDSISPEDAGSYSCWVNNSIGQTASKAWTLEVLYAPRRLRVSMSPGDQVMEGKSATLTCESDANPPVSHYTWF DWNNQSLPYHSQKLRLEPVKVQHSGAYWCQGTNSVGKGRSPLSTLTVYYSPETIGRRVAVGLGSCLAILILAICGLKLQRRWKRTQSQQG LQENSSGQSFFVRNKKVRRAPLSEGPHSLGCYNPMMEDGISYTTLRFPEMNIPRTGDAESSEMQRPPPDCDDTVTYSALHKRQVGDYENV
P20273-2	MHLLGPWLLLLVLEYLAFSDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKNTSKFDGTRLYESTKDGKVPSEQK RVQFLGDKNKNCTLSIHPVHLNDSGQLGLRMESKTEKWMERIHLNVSERPFPPHIQLPPEIQESQEVTLTCLLNFSCYGYPIQLQWLLEG VPMRQAAVTSTSLTIKSVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSNDTVQLNVKHPPKKVTTVIQNPMPIREGDTVTLSCNYNSS NPSVTRYEWKPHGAWEEPSLGVLKIQNVGWDNTTIACAACNSWCSWASPVALNVQYAPRDVRVRKIKPLSEIHSGNSVSLQCDFSSSHPK EVQFFWEKNGRLLGKESQLNFDSISPEDAGSYSCWVNNSIGQTASKAWTLEVLYAPRRLRVSMSPGDQVMEGKSATLTCESDANPPVSHY TWFDWNNQSLPYHSQKLRLEPVKVQHSGAYWCQGTNSVGKGRSPLSTLTVYYSPETIGRRVAVGLGSCLAILILAICGLKLQRRWKRTQS QQGLQENSSGQSFFVRNKKVRRAPLSEGPHSLGCYNPMMEDGISYTTLRFPEMNIPRTGDAESSEMQRPPPDCDDTVTYSALHKRQVGDY
P20273-3	MHLLGPWLLLLVLEYLAFSDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKNTSKFDGTRLYESTKDGKVPSEQK RVQFLGDKNKNCTLSIHPVHLNDSGQLGLRMESKTEKWMERIHLNVSERPFPPHIQLPPEIQESQEVTLTCLLNFSCYGYPIQLQWLLEG VPMRQAAVTSTSLTIKSVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSNDTVQLNVKHTPKLEIKVTPSDAIVREGDSVTMTCEVSSS NPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVGPGRSEEVFLQVQYPPKKVTTVIQNPMPIREGDTVTLSCNYNSSN PSVTRYEWKPHGAWEEPSLGVLKIQNVGWDNTTIACAACNSWCSWASPVALNVQYAPRDVRVRKIKPLSEIHSGNSVSLQCDFSSSHPKE VQFFWEKNGRLLGKESQLNFDSISPEDAGSYSCWVNNSIGQTASKAWTLEVLYAPRRLRVSMSPGDQVMEGKSATLTCESDANPPVSHYT WFDWNNQSLPYHSQKLRLEPVKVQHSGAYWCQGTNSVGKGRSPLSTLTVYYSPETIGRRVAVGLGSCLAILILAICGLKLQRRWKRTQSQ QGLQENSSGQSFFVRNKKVRRAPLSEGPHSLGCYNPMMEDGISYTTLRFPEMNIPRTGDAESSEMQRPPPDCDDTVTYSALHKRQVGDYE
P20273-4	MHLLGPWLLLLVLEYLAFSDSSKWVFEHPETLYAWEGACVWIPCTYRALDGDLESFILFHNPEYNKNTSKFDGTRLYESTKDGKVPSEQK RVQFLGDKNKNCTLSIHPVHLNDSGQLGLRMESKTEKWMERIHLNVSERPFPPHIQLPPEIQESQEVTLTCLLNFSCYGYPIQLQWLLEG VPMRQAAVTSTSLTIKSVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSNDTVQLNVKHTPKLEIKVTPSDAIVREGDSVTMTCEVSSS NPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVGPGRSEEVFLQVQYAPEPSTVQILHSPAVEGSQVEFLCMSLANPL PTNYTWYHNGKEMQGRTEEKVHIPKILPWHAGTYSCVAENILGTGQRGPGAELDVQYPPKKVTTVIQNPMPIREGDTVTLSCNYNSSNPS VTRYEWKPHGAWEEPSLGVLKIQNVGWDNTTIACAACNSWCSWASPVALNVQYAPRDVRVRKIKPLSEIHSGNSVSLQCDFSSSHPKEVQ FFWEKNGRLLGKESQLNFDSISPEDAGSYSCWVNNSIGQTASKAWTLEVLYAPRRLRVSMSPGDQVMEGKSATLTCESDANPPVSHYTWF DWNNQSLPYHSQKLRLEPVKVQHSGAYWCQGTNSVGKGRSPLSTLTVYYSPETIGRRVAVGLGSCLAILILAICGLKLQRRWKRTQSQQG
P20273-5	MSLWLLEGVPMRQAAVTSTSLTIKSVFTRSELKFSPQWSHHGKIVTCQLQDADGKFLSNDTVQLNVKHTPKLEIKVTPSDAIVREGDSVT MTCEVSSSNPEYTTVSWLKDGTSLKKQNTFTLNLREVTKDQSGKYCCQVSNDVGPGRSEEVFLQVQYAPEPSTVQILHSPAVEGSQVEFL CMSLANPLPTNYTWYHNGKEMQGRTEEKVHIPKILPWHAGTYSCVAENILGTGQRGPGAELDVQYPPKKVTTVIQNPMPIREGDTVTLSC NYNSSNPSVTRYEWKPHGAWEEPSLGVLKIQNVGWDNTTIACAACNSWCSWASPVALNVQYAPRDVRVRKIKPLSEIHSGNSVSLQCDFS SSHPKEVQFFWEKNGRLLGKESQLNFDSISPEDAGSYSCWVNNSIGQTASKAWTLEVLYAPRRLRVSMSPGDQVMEGKSATLTCESDANP PVSHYTWFDWNNQSLPYHSQKLRLEPVKVQHSGAYWCQGTNSVGKGRSPLSTLTVYYSPETIGRRVAVGLGSCLAILILAICGLKLQRRW KRTQSQQGLQENSSGQSFFVRNKKVRRAPLSEGPHSLGCYNPMMEDGISYTTLRFPEMNIPRTGDAESSEMQRPPPDCDDTVTYSALHKR

Protein Functional Features

Main function of this protein. (from UniProt)

CD22 (go to UniProt):P20273

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
P20273	Topological domain	20	687	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=241;End=417
P20273	Topological domain	20	687	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=330;End=417
P20273	Topological domain	20	687	Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=4;End=175
P20273	Topological domain	707	847	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=737;End=751
P20273	Topological domain	707	847	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=752;End=847
P20273	Domain	20	138	Note=Ig-like V-type	Type=Deletion;Start=4;End=175
P20273	Domain	143	235	Note=Ig-like C2-type 1	Type=Deletion;Start=4;End=175
P20273	Domain	242	326	Note=Ig-like C2-type 2	Type=Deletion;Start=241;End=417
P20273	Domain	331	416	Note=Ig-like C2-type 3	Type=Deletion;Start=241;End=417
P20273	Domain	331	416	Note=Ig-like C2-type 3	Type=Deletion;Start=330;End=417
P20273	Motif	760	765	Note=ITIM motif 1	Type=Deletion;Start=752;End=847
P20273	Motif	794	799	Note=ITIM motif 2	Type=Deletion;Start=752;End=847
P20273	Motif	820	825	Note=ITIM motif 3	Type=Deletion;Start=752;End=847
P20273	Motif	840	845	Note=ITIM motif 4	Type=Deletion;Start=752;End=847

Gene Isoform Structures and Expression Levels for CD22

Gene structures of our canonical and alternative spliced genes of CD22
* 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 P20273-1

3D view using mol* of P20273-2

3D view using mol* of P20273-3

3D view using mol* of P20273-4

3D view using mol* of P20273-5

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 P20273-1

pLDDT distribution across the protein length of P20273-2

pLDDT distribution across the protein length of P20273-3

pLDDT distribution across the protein length of P20273-4

pLDDT distribution across the protein length of P20273-5

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 P20273-1

Ramachandran plot of P20273-2

Ramachandran plot of P20273-3

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
P20273-1	0.697	43	0.673	121.765	0.784	0.579	0.743	0.133	0.892	0.149	0.677	29,30,31,32,33,141,142,143,144,163,164,165,166,196 ,197,198,199
P20273-2	0.818	70	0.821	116.277	0.565	0.582	0.862	0.241	0.964	0.25	1.295	571,572,573,574,575,576,579,581,582,583,584,585,58 6,587
P20273-3	0.821	71	0.772	138.915	0.542	0.603	0.871	0.207	1.171	0.177	0.516	672,673,674,675,676,677,678,679,704,705,706,707,70 8,709,710
P20273-4	0.617	28	0.566	67.571	0.696	0.598	0.773	0.446	0.892	0.5	0.344	165,166,167,168,169,170,171,172,191,193,200
P20273-5	0.626	24	0.601	87.122	0.784	0.583	0.707	0.571	0.642	0.889	0.639	2,28,29,30,47,48,49,58,59,60

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 P20273-1_P20273-1_5vkj_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 P20273-1_5vkj_A_P20273-2.pdb

3D view using mol* of P20273-1_5vkj_A_P20273-3.pdb

3D view using mol* of P20273-1_5vkj_A_P20273-4.pdb

3D view using mol* of P20273-1_5vkj_A_P20273-5.pdb

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

3D view using mol* of P20273-1_P20273-2.pdb

3D view using mol* of P20273-1_P20273-3.pdb

3D view using mol* of P20273-1_P20273-4.pdb

3D view using mol* of P20273-1_P20273-5.pdb

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

./stats/secondary_structure/figure/P20273-1_vs_P20273-2.png

./stats/secondary_structure/figure/P20273-1_vs_P20273-3.png

./stats/secondary_structure/figure/P20273-1_vs_P20273-4.png

./stats/secondary_structure/figure/P20273-1_vs_P20273-5.png

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

./stats/relative_asa/P20273-1_vs_P20273-2.png

./stats/relative_asa/P20273-1_vs_P20273-3.png

./stats/relative_asa/P20273-1_vs_P20273-4.png

./stats/relative_asa/P20273-1_vs_P20273-5.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 CD22

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P20273	CD22	DB04958	Epratuzumab	investigational	antibody, regulator
P20273	CD22	DB12688	Moxetumomab pasudotox	approved, investigational	binder, antibody, regulator
P20273	CD22	DB05889	Inotuzumab ozogamicin	approved, investigational	antibody, regulator

Related Diseases to CD22

Previous studies relating to the alternative splicing of CD22 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CD22

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance