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:SENP7

Protein Summary

Gene summary

Gene name: SENP7
ASpdb.0 ID: 57337
	Gene
Gene symbol	SENP7
Gene ID	57337
Gene name	SUMO specific peptidase 7
Synonyms	-
Cytomap	3q12.3
Type of gene	protein-coding
Description	sentrin-specific protease 7SUMO-1-specific protease 2SUMO1/sentrin specific peptidase 7sentrin/SUMO-specific protease SENP7
Modification date	20240403
UniProtAcc	Q9BQF6

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	SENP7	GO:0005634	nucleus	-

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
Q9BQF6-1	Q9BQF6-1_3eay_A.pdb	3EAY	X-ray	2.4	A	744	1047

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

Q9BQF6

SENP7

Q9BQF6-1

Q9BQF6-3

1050

238

812

Deletion

none

Q9BQF6

SENP7

Q9BQF6-1

Q9BQF6-3

1050

238

813

827

Substitution

TRKENNLTEDNPNLS

MKKFLYIKSVFHTLR

Q9BQF6

SENP7

Q9BQF6-1

Q9BQF6-4

1050

886

Deletion

none

Q9BQF6

SENP7

Q9BQF6-1

Q9BQF6-4

1050

886

225

Deletion

none

Q9BQF6

SENP7

Q9BQF6-1

Q9BQF6-5

1050

984

160

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced SENP7

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of SENP7

UniProt-id	ENSG	ENST	ENSP
Q9BQF6-1	ENSG00000138468.16	ENST00000394095.7	ENSP00000377655.2
Q9BQF6-3	ENSG00000138468.16	ENST00000394085.7	ENSP00000377647.3
Q9BQF6-4	ENSG00000138468.16	ENST00000394091.5	ENSP00000377651.1
Q9BQF6-5	ENSG00000138468.16	ENST00000314261.11	ENSP00000313624.7

UniProt-id	NM ID	NP ID
Q9BQF6-1	NM_020654.4	NP_065705.3
Q9BQF6-4	NM_001282803.1	NP_001269732.1
Q9BQF6-5	NM_001282801.1	NP_001269730.1

Amino acid sequences of our canonical and alternatively spliced SENP7

accession_id	Protein sequence
Q9BQF6-1	MDKRKLGRRPSSSEIITEGKRKKSSSDLSEIRKMLNAKPEDVHVQSPLSKFRSSERWTLPLQWERSLRNKVISLDHKNKKHIRGCPVTSK SSPERQLKVMLTNVLWTDLGRKFRKTLPRNDANLCDANKVQSDSLPSTSVDSLETCQKLEPLRQSLNLSERIPRVILTNVLGTELGRKYI RTPPVTEGSLSDTDNLQSEQLSSSSDGSLESYQNLNPHKSCYLSERGSQRSKTVDDNSAKQTAHNKEKRRKDDGISLLISDTQPEDLNSG SRGCDHLEQESRNKDVKYSDSKVELTLISRKTKRRLRNNLPDSQYCTSLDKSTEQTKKQEDDSTISTEFEKPSENYHQDPKLPEEITTKP TKSDFTKLSSLNSQELTLSNATKSASAGSTTETVENSNSIDIVGISSLVEKDENELNTIEKPILRGHNEGNQSLISAEPIVVSSDEEGPV EHKSSEILKLQSKQDRETTNENESTSESALLELPLITCESVQMSSELCPYNPVMENISSIMPSNEMDLQLDFIFTSVYIGKIKGASKGCV TITKKYIKIPFQVSLNEISLLVDTTHLKRFGLWKSKDDNHSKRSHAILFFWVSSDYLQEIQTQLEHSVLSQQSKSSEFIFLELHNPVSQR EELKLKDIMTEISIISGELELSYPLSWVQAFPLFQNLSSKESSFIHYYCVSTCSFPAGVAVAEEMKLKSVSQPSNTDAAKPTYTFLQKQS SGCYSLSITSNPDEEWREVRHTGLVQKLIVYPPPPTKGGLGVTNEDLECLEEGEFLNDVIIDFYLKYLILEKASDELVERSHIFSSFFYK CLTRKENNLTEDNPNLSMAQRRHKRVRTWTRHINIFNKDYIFVPVNESSHWYLAVICFPWLEEAVYEDFPQTVSQQSQAQQSQNDNKTID NDLRTTSTLSLSAEDSQSTESNMSVPKKMCKRPCILILDSLKAASVQNTVQNLREYLEVEWEVKLKTHRQFSKTNMVDLCPKVPKQDNSS
Q9BQF6-3	MKKFLYIKSVFHTLRMAQRRHKRVRTWTRHINIFNKDYIFVPVNESSHWYLAVICFPWLEEAVYEDFPQTVSQQSQAQQSQNDNKTIDND LRTTSTLSLSAEDSQSTESNMSVPKKMCKRPCILILDSLKAASVQNTVQNLREYLEVEWEVKLKTHRQFSKTNMVDLCPKVPKQDNSSDC
Q9BQF6-4	MLNAKPEDVHVQSPLSKFRSSERWTLPLQWERSLRNKVISLDHKNKKHIRGCPVTSKSSPERGSQRSKTVDDNSAKQTAHNKEKRRKDDG ISLLISDTQPEDLNSGSRGCDHLEQESRNKDVKYSDSKVELTLISRKTKRRLRNNLPDSQYCTSLDKSTEQTKKQEDDSTISTEFEKPSE NYHQDPKLPEEITTKPTKSDFTKLSSLNSQELTLSNATKSASAGSTTETVENSNSIDIVGISSLVEKDENELNTIEKPILRGHNEGNQSL ISAEPIVVSSDEEGPVEHKSSEILKLQSKQDRETTNENESTSESALLELPLITCESVQMSSELCPYNPVMENISSIMPSNEMDLQLDFIF TSVYIGKIKGASKGCVTITKKYIKIPFQVSLNEISLLVDTTHLKRFGLWKSKDDNHSKRSHAILFFWVSSDYLQEIQTQLEHSVLSQQSK SSEFIFLELHNPVSQREELKLKDIMTEISIISGELELSYPLSWVQAFPLFQNLSSKESSFIHYYCVSTCSFPAGVAVAEEMKLKSVSQPS NTDAAKPTYTFLQKQSSGCYSLSITSNPDEEWREVRHTGLVQKLIVYPPPPTKGGLGVTNEDLECLEEGEFLNDVIIDFYLKYLILEKAS DELVERSHIFSSFFYKCLTRKENNLTEDNPNLSMAQRRHKRVRTWTRHINIFNKDYIFVPVNESSHWYLAVICFPWLEEAVYEDFPQTVS QQSQAQQSQNDNKTIDNDLRTTSTLSLSAEDSQSTESNMSVPKKMCKRPCILILDSLKAASVQNTVQNLREYLEVEWEVKLKTHRQFSKT
Q9BQF6-5	MDKRKLGRRPSSSEIITEGKRKKSSSDLSEIRKMLNAKPEDVHVQSPLSKFRSSERWTLPLQWERSLRNKVISLDHKNKKHIRGCPVTSK SSPERIPRVILTNVLGTELGRKYIRTPPVTEGSLSDTDNLQSEQLSSSSDGSLESYQNLNPHKSCYLSERGSQRSKTVDDNSAKQTAHNK EKRRKDDGISLLISDTQPEDLNSGSRGCDHLEQESRNKDVKYSDSKVELTLISRKTKRRLRNNLPDSQYCTSLDKSTEQTKKQEDDSTIS TEFEKPSENYHQDPKLPEEITTKPTKSDFTKLSSLNSQELTLSNATKSASAGSTTETVENSNSIDIVGISSLVEKDENELNTIEKPILRG HNEGNQSLISAEPIVVSSDEEGPVEHKSSEILKLQSKQDRETTNENESTSESALLELPLITCESVQMSSELCPYNPVMENISSIMPSNEM DLQLDFIFTSVYIGKIKGASKGCVTITKKYIKIPFQVSLNEISLLVDTTHLKRFGLWKSKDDNHSKRSHAILFFWVSSDYLQEIQTQLEH SVLSQQSKSSEFIFLELHNPVSQREELKLKDIMTEISIISGELELSYPLSWVQAFPLFQNLSSKESSFIHYYCVSTCSFPAGVAVAEEMK LKSVSQPSNTDAAKPTYTFLQKQSSGCYSLSITSNPDEEWREVRHTGLVQKLIVYPPPPTKGGLGVTNEDLECLEEGEFLNDVIIDFYLK YLILEKASDELVERSHIFSSFFYKCLTRKENNLTEDNPNLSMAQRRHKRVRTWTRHINIFNKDYIFVPVNESSHWYLAVICFPWLEEAVY EDFPQTVSQQSQAQQSQNDNKTIDNDLRTTSTLSLSAEDSQSTESNMSVPKKMCKRPCILILDSLKAASVQNTVQNLREYLEVEWEVKLK

Protein Functional Features

Main function of this protein. (from UniProt)

SENP7 (go to UniProt):Q9BQF6

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
Q9BQF6	Region	1	28	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Region	1	28	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=33
Q9BQF6	Region	183	288	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Region	183	288	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=95;End=225
Q9BQF6	Region	304	365	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Region	443	476	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Region	760	1050	Note=Protease;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9HC62	Type=Deletion;Start=1;End=812
Q9BQF6	Region	760	1050	Note=Protease;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9HC62	Type=Substitution;Start=813;End=827
Q9BQF6	Compositional bias	186	228	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Compositional bias	186	228	Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=95;End=225
Q9BQF6	Compositional bias	229	256	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Compositional bias	271	288	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Compositional bias	323	361	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812
Q9BQF6	Compositional bias	445	472	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=812

Gene Isoform Structures and Expression Levels for SENP7

Gene structures of our canonical and alternative spliced genes of SENP7
* 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 Q9BQF6-1

3D view using mol* of Q9BQF6-3

3D view using mol* of Q9BQF6-4

3D view using mol* of Q9BQF6-5

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 Q9BQF6-1

pLDDT distribution across the protein length of Q9BQF6-3

pLDDT distribution across the protein length of Q9BQF6-4

pLDDT distribution across the protein length of Q9BQF6-5

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 Q9BQF6-1

Ramachandran plot of Q9BQF6-3

Ramachandran plot of Q9BQF6-5

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
Q9BQF6-1	1.082	128	1.126	293.951	0.563	0.757	0.972	1.214	0.821	1.48	0.904	573,574,575,577,578,580,581,582,583,584,585,586,58 7,622,657,658,661,674,678,681,682,683,684,685,686
Q9BQF6-3	0.79	60	0.782	171.157	0.709	0.604	0.733	0.211	0.945	0.224	1.045	186,189,190,193,194,195,196,197,198,200,202,203,20 4,205,208,209,210,213
Q9BQF6-4	1.094	126	1.159	226.037	0.558	0.735	0.98	1.52	0.681	2.232	1.15	409,410,411,414,416,417,418,419,421,422,423,493,49 7,501,502,503,504,510,511,514,515,516,517,518,519
Q9BQF6-5	1.115	146	1.177	228.095	0.469	0.769	1.026	1.607	0.69	2.33	1.072	507,508,509,511,512,514,515,516,517,519,520,521,59 1,592,595,599,608,612,613,615,616,617,667

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 Q9BQF6-1_Q9BQF6-1_3eay_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 Q9BQF6-1_3eay_A_Q9BQF6-3.pdb

3D view using mol* of Q9BQF6-1_3eay_A_Q9BQF6-4.pdb

3D view using mol* of Q9BQF6-1_3eay_A_Q9BQF6-5.pdb

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

3D view using mol* of Q9BQF6-1_Q9BQF6-3.pdb

3D view using mol* of Q9BQF6-1_Q9BQF6-4.pdb

3D view using mol* of Q9BQF6-1_Q9BQF6-5.pdb

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

./stats/secondary_structure/figure/Q9BQF6-1_vs_Q9BQF6-3.png

./stats/secondary_structure/figure/Q9BQF6-1_vs_Q9BQF6-4.png

./stats/secondary_structure/figure/Q9BQF6-1_vs_Q9BQF6-5.png

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

./stats/relative_asa/Q9BQF6-1_vs_Q9BQF6-3.png

./stats/relative_asa/Q9BQF6-1_vs_Q9BQF6-4.png

./stats/relative_asa/Q9BQF6-1_vs_Q9BQF6-5.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 SENP7

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to SENP7

Previous studies relating to the alternative splicing of SENP7 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in SENP7

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance