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:CEP63

Protein Summary

Gene summary

Gene name: CEP63
ASpdb.0 ID: 80254
	Gene
Gene symbol	CEP63
Gene ID	80254
Gene name	centrosomal protein 63
Synonyms	SCKL6
Cytomap	3q22.2
Type of gene	protein-coding
Description	centrosomal protein of 63 kDacentrosomal protein 63kDacentrosome protein CEP63
Modification date	20240403
UniProtAcc	Q96MT8

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CEP63	GO:0005813	centrosome	35793002
Gene	CEP63	GO:0005813	centrosome	14654843\|21399614
Gene	CEP63	GO:0045824	negative regulation of innate immune response	35793002
Gene	CEP63	GO:0050821	protein stabilization	35989368
Gene	CEP63	GO:0060090	molecular adaptor activity	35793002
Gene	CEP63	GO:1900045	negative regulation of protein K63-linked ubiquitination	35989368

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
Q96MT8-1	Q96MT8-1_6csv_A.pdb	6CSV	X-ray	2.5	A	664	703

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

Q96MT8

CEP63

Q96MT8-1

Q96MT8-2

703

541

490

651

Deletion

none

489

Q96MT8

CEP63

Q96MT8-1

Q96MT8-3

703

495

310

355

Deletion

none

309

Q96MT8

CEP63

Q96MT8-1

Q96MT8-3

703

495

490

651

Deletion

none

443

Q96MT8

CEP63

Q96MT8-1

Q96MT8-4

703

475

310

355

Deletion

none

309

Q96MT8

CEP63

Q96MT8-1

Q96MT8-4

703

475

490

521

Substitution

AKEISLADLQENYIEALNKLVSENQQLQKDLM

RWGFTMLSSLVLNFGIQAIRQPQRPKVLELQV

444

475

Q96MT8

CEP63

Q96MT8-1

Q96MT8-4

703

475

522

703

Deletion

none

475

Multiple sequence alignment of our canonical and alternatively spliced CEP63

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CEP63

UniProt-id	ENSG	ENST	ENSP
Q96MT8-1	ENSG00000182923.20	ENST00000513612.7	ENSP00000426129.1
Q96MT8-1	ENSG00000182923.20	ENST00000606977.5	ENSP00000475903.1
Q96MT8-1	ENSG00000182923.20	ENST00000675561.1	ENSP00000502085.1
Q96MT8-1	ENSG00000182923.20	ENST00000683596.1	ENSP00000506896.1
Q96MT8-2	ENSG00000182923.20	ENST00000383229.8	ENSP00000372716.3
Q96MT8-2	ENSG00000182923.20	ENST00000683608.1	ENSP00000507704.1
Q96MT8-2	ENSG00000182923.20	ENST00000684217.1	ENSP00000508291.1
Q96MT8-2	ENSG00000182923.20	ENST00000684677.1	ENSP00000507217.1
Q96MT8-3	ENSG00000182923.20	ENST00000332047.10	ENSP00000328382.5
Q96MT8-3	ENSG00000182923.20	ENST00000682042.1	ENSP00000507228.1
Q96MT8-3	ENSG00000182923.20	ENST00000682800.1	ENSP00000506791.1
Q96MT8-3	ENSG00000182923.20	ENST00000682858.1	ENSP00000507703.1
Q96MT8-3	ENSG00000182923.20	ENST00000683177.1	ENSP00000506828.1
Q96MT8-3	ENSG00000182923.20	ENST00000683861.1	ENSP00000506728.1
Q96MT8-4	ENSG00000182923.20	ENST00000354446.7	ENSP00000346432.3
Q96MT8-4	ENSG00000182923.20	ENST00000512894.6	ENSP00000423225.2
Q96MT8-4	ENSG00000182923.20	ENST00000620544.5	ENSP00000482219.1

UniProt-id	NM ID	NP ID
Q96MT8-1	NM_025180.3	NP_079456.2
Q96MT8-1	XM_005247797.3	XP_005247854.1
Q96MT8-1	XM_006713760.3	XP_006713823.1
Q96MT8-2	NM_001042400.1	NP_001035859.1
Q96MT8-3	NM_001042383.1	NP_001035842.1
Q96MT8-4	NM_001042384.1	NP_001035843.1

Amino acid sequences of our canonical and alternatively spliced CEP63

accession_id	Protein sequence
Q96MT8-1	MEALLEGIQNRGHGGGFLTSCEAELQELMKQIDIMVAHKKSEWEGRTHALETCLKIREQELKSLRSQLDVTHKEVGMLHQQVEEHEKIKQ EMTMEYKQELKKLHEELCILKRSYEKLQKKQMREFRGNTKNHREDRSEIERLTAKIEEFRQKSLDWEKQRLIYQQQVSSLEAQRKALAEQ SEIIQAQLVNRKQKLESVELSSQSEIQHLSSKLERANDTICANELEIERLTMRVNDLVGTSMTVLQEQQQKEEKLRESEKLLEALQEEKR ELKAALQSQENLIHEARIQKEKLQEKVKATNTQHAVEAIRPREESLAEKKYTSQGQGDLDSVLSQLNFTHTSEDLLQAEVTCLEGSLESV SATCKQLSQELMEKYEELKRMEAHNNEYKAEIKKLKEQILQGEQSYSSALEGMKMEISHLTQELHQRDITIASTKGSSSDMEKRLRAEMQ KAEDKAVEHKEILDQLESLKLENRHLSEMVMKLELGLHEAKEISLADLQENYIEALNKLVSENQQLQKDLMNTKSQLEISTQMCKKQNDR IFKPTHSRTTEFKNTEFKPTHGQHRHDGIKTEHYKTDLHSPRGQASDSINPMSRVLSPLSPQISPCSSTRSLTSYSLCKTHSLPSALDTN
Q96MT8-2	MEALLEGIQNRGHGGGFLTSCEAELQELMKQIDIMVAHKKSEWEGRTHALETCLKIREQELKSLRSQLDVTHKEVGMLHQQVEEHEKIKQ EMTMEYKQELKKLHEELCILKRSYEKLQKKQMREFRGNTKNHREDRSEIERLTAKIEEFRQKSLDWEKQRLIYQQQVSSLEAQRKALAEQ SEIIQAQLVNRKQKLESVELSSQSEIQHLSSKLERANDTICANELEIERLTMRVNDLVGTSMTVLQEQQQKEEKLRESEKLLEALQEEKR ELKAALQSQENLIHEARIQKEKLQEKVKATNTQHAVEAIRPREESLAEKKYTSQGQGDLDSVLSQLNFTHTSEDLLQAEVTCLEGSLESV SATCKQLSQELMEKYEELKRMEAHNNEYKAEIKKLKEQILQGEQSYSSALEGMKMEISHLTQELHQRDITIASTKGSSSDMEKRLRAEMQ KAEDKAVEHKEILDQLESLKLENRHLSEMVMKLELGLHECSLPVSPLGSIATRFLEEEELRSHHILERLDAHIEELKRESEKTVRQFTAL
Q96MT8-3	MEALLEGIQNRGHGGGFLTSCEAELQELMKQIDIMVAHKKSEWEGRTHALETCLKIREQELKSLRSQLDVTHKEVGMLHQQVEEHEKIKQ EMTMEYKQELKKLHEELCILKRSYEKLQKKQMREFRGNTKNHREDRSEIERLTAKIEEFRQKSLDWEKQRLIYQQQVSSLEAQRKALAEQ SEIIQAQLVNRKQKLESVELSSQSEIQHLSSKLERANDTICANELEIERLTMRVNDLVGTSMTVLQEQQQKEEKLRESEKLLEALQEEKR ELKAALQSQENLIHEARIQKEKLQEKVKATNTQHAVEAISLESVSATCKQLSQELMEKYEELKRMEAHNNEYKAEIKKLKEQILQGEQSY SSALEGMKMEISHLTQELHQRDITIASTKGSSSDMEKRLRAEMQKAEDKAVEHKEILDQLESLKLENRHLSEMVMKLELGLHECSLPVSP
Q96MT8-4	MEALLEGIQNRGHGGGFLTSCEAELQELMKQIDIMVAHKKSEWEGRTHALETCLKIREQELKSLRSQLDVTHKEVGMLHQQVEEHEKIKQ EMTMEYKQELKKLHEELCILKRSYEKLQKKQMREFRGNTKNHREDRSEIERLTAKIEEFRQKSLDWEKQRLIYQQQVSSLEAQRKALAEQ SEIIQAQLVNRKQKLESVELSSQSEIQHLSSKLERANDTICANELEIERLTMRVNDLVGTSMTVLQEQQQKEEKLRESEKLLEALQEEKR ELKAALQSQENLIHEARIQKEKLQEKVKATNTQHAVEAISLESVSATCKQLSQELMEKYEELKRMEAHNNEYKAEIKKLKEQILQGEQSY SSALEGMKMEISHLTQELHQRDITIASTKGSSSDMEKRLRAEMQKAEDKAVEHKEILDQLESLKLENRHLSEMVMKLELGLHERWGFTML

Protein Functional Features

Main function of this protein. (from UniProt)

CEP63 (go to UniProt):Q96MT8

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
Q96MT8	Coiled coil	353	533	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=490;End=651
Q96MT8	Coiled coil	353	533	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=310;End=355
Q96MT8	Coiled coil	353	533	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=490;End=651
Q96MT8	Coiled coil	353	533	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=310;End=355
Q96MT8	Coiled coil	353	533	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=490;End=521
Q96MT8	Coiled coil	353	533	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=522;End=703
Q96MT8	Coiled coil	676	703	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=522;End=703

Gene Isoform Structures and Expression Levels for CEP63

Gene structures of our canonical and alternative spliced genes of CEP63
* 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 Q96MT8-1

3D view using mol* of Q96MT8-2

3D view using mol* of Q96MT8-3

3D view using mol* of Q96MT8-4

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 Q96MT8-1

pLDDT distribution across the protein length of Q96MT8-2

pLDDT distribution across the protein length of Q96MT8-3

pLDDT distribution across the protein length of Q96MT8-4

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 Q96MT8-1

Ramachandran plot of Q96MT8-2

Ramachandran plot of Q96MT8-3

Ramachandran plot of Q96MT8-4

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
Q96MT8-1	0.424	12	0.321	37.044	0.789	0.547	0.752	0.035	1.02	0.034	2.459	8,9,11,12,13,14,15,18,19,22
Q96MT8-2	0.858	67	0.894	169.099	0.685	0.583	0.769	0.974	0.69	1.411	2.337	1,4,5,8,9,11,12,14,15,18,19,21,22,25,26,29,30,32,3 3
Q96MT8-3	0.585	19	0.538	53.165	0.725	0.602	0.761	0.97	0.716	1.354	8.521	5,8,9,22,25,26,29
Q96MT8-4	0.701	19	0.69	49.049	0.596	0.687	0.985	2.275	0.406	5.597	1.043	4,5,8,18,21,22,25,26,29

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 Q96MT8-1_Q96MT8-1_6csv_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 Q96MT8-1_6csv_A_Q96MT8-2.pdb

3D view using mol* of Q96MT8-1_6csv_A_Q96MT8-3.pdb

3D view using mol* of Q96MT8-1_6csv_A_Q96MT8-4.pdb

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

3D view using mol* of Q96MT8-1_Q96MT8-2.pdb

3D view using mol* of Q96MT8-1_Q96MT8-3.pdb

3D view using mol* of Q96MT8-1_Q96MT8-4.pdb

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

./stats/secondary_structure/figure/Q96MT8-1_vs_Q96MT8-2.png

./stats/secondary_structure/figure/Q96MT8-1_vs_Q96MT8-3.png

./stats/secondary_structure/figure/Q96MT8-1_vs_Q96MT8-4.png

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

./stats/relative_asa/Q96MT8-1_vs_Q96MT8-2.png

./stats/relative_asa/Q96MT8-1_vs_Q96MT8-3.png

./stats/relative_asa/Q96MT8-1_vs_Q96MT8-4.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 CEP63

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to CEP63

Previous studies relating to the alternative splicing of CEP63 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CEP63

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance