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:IL24

Protein Summary

Gene summary

Gene name: IL24
ASpdb.0 ID: 11009
	Gene
Gene symbol	IL24
Gene ID	11009
Gene name	interleukin 24
Synonyms	C49A\|FISP\|IL10B\|MDA7\|MOB5\|ST16
Cytomap	1q32.1
Type of gene	protein-coding
Description	interleukin-24IL-4-induced secreted proteinmelanocyte-associated Mda-7melanoma differentiation-associated gene 7 proteinsuppression of tumorigenicity 16 (melanoma differentiation)
Modification date	20240305
UniProtAcc	Q13007

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

Partner

Gene

GO ID

GO term

PubMed ID

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
Q13007-1	Q13007-1_6df3_C.pdb	6DF3	X-ray	2.15	C	52	206

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

Q13007

IL24

Q13007-1

Q13007-2

206

207

Substitution

Q13007

IL24

Q13007-1

Q13007-3

206

154

Substitution

Q13007

IL24

Q13007-1

Q13007-3

206

154

101

153

Deletion

none

101

Q13007

IL24

Q13007-1

Q13007-4

206

Substitution

RPFCPPLLATASQMQMVVLPCLGFTLLLWSQVSGAQGQEFHFGPCQVKGVVPQKLWEAFWAVKDTMQAQDNITSARLLQQEVLQNVSDAESCYLVHTLLEFYLKTVFKNYHNRTVEVRTLKSFSTLANNFVLIVSQLQPSQENEMFSIRDSAHRRFLLFRRAFKQLDVEAALTKALGEVDILLTWMQKFYKL

SKLRITSRVPGCCSRRFCRTSRKKMRCFPSETVHTGGFCYSGEHSNSWT

Multiple sequence alignment of our canonical and alternatively spliced IL24

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of IL24

UniProt-id	ENSG	ENST	ENSP
Q13007-1	ENSG00000162892.16	ENST00000294984.7	ENSP00000294984.2
Q13007-2	ENSG00000162892.16	ENST00000391929.7	ENSP00000375795.3
Q13007-3	ENSG00000162892.16	ENST00000367093.3	ENSP00000356060.3
Q13007-4	ENSG00000162892.16	ENST00000611909.4	ENSP00000484900.1

UniProt-id	NM ID	NP ID
Q13007-1	NM_006850.3	NP_006841.1
Q13007-2	NM_001185156.1	NP_001172085.1
Q13007-3	NM_001185157.1	NP_001172086.1
Q13007-4	NM_001185158.1	NP_001172087.1

Amino acid sequences of our canonical and alternatively spliced IL24

accession_id	Protein sequence
Q13007-1	MNFQQRLQSLWTLARPFCPPLLATASQMQMVVLPCLGFTLLLWSQVSGAQGQEFHFGPCQVKGVVPQKLWEAFWAVKDTMQAQDNITSAR LLQQEVLQNVSDAESCYLVHTLLEFYLKTVFKNYHNRTVEVRTLKSFSTLANNFVLIVSQLQPSQENEMFSIRDSAHRRFLLFRRAFKQL
Q13007-2	MNFQQRLQSLWTLASRPFCPPLLATASQMQMVVLPCLGFTLLLWSQVSGAQGQEFHFGPCQVKGVVPQKLWEAFWAVKDTMQAQDNITSA RLLQQEVLQNVSDAESCYLVHTLLEFYLKTVFKNYHNRTVEVRTLKSFSTLANNFVLIVSQLQPSQENEMFSIRDSAHRRFLLFRRAFKQ
Q13007-3	MNFQQRLQSLWTLASRPFCPPLLATASQMQMVVLPCLGFTLLLWSQVSGAQGQEFHFGPCQVKGVVPQKLWEAFWAVKDTMQAQDNITSA
Q13007-4

Protein Functional Features

Main function of this protein. (from UniProt)

IL24 (go to UniProt):Q13007

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

Gene Isoform Structures and Expression Levels for IL24

Gene structures of our canonical and alternative spliced genes of IL24
* 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 Q13007-1

3D view using mol* of Q13007-2

3D view using mol* of Q13007-3

3D view using mol* of Q13007-4

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 Q13007-1

pLDDT distribution across the protein length of Q13007-2

pLDDT distribution across the protein length of Q13007-3

pLDDT distribution across the protein length of Q13007-4

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 Q13007-1

Ramachandran plot of Q13007-2

Ramachandran plot of Q13007-3

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
Q13007-1	0.647	36	0.611	88.837	0.712	0.568	0.811	0.59	0.901	0.656	0.507	90,94,97,98,99,100,195,198,199,202,203
Q13007-2	0.763	28	0.798	69.972	0.75	0.628	0.716	1.724	0.234	7.369	5.299	118,122,123,125,126,129,135,138,139,142
Q13007-3	0.894	47	0.961	196.882	0.674	0.649	0.803	2.302	0.224	10.297	2.123	57,58,93,97,98,101,114,117,118,121,144,147,151
Q13007-4	0.682	41	0.476	63.112	0.549	0.617	0.919	0.037	1.52	0.024	0.982	21,22,23,24,25,26,27,28,43,45,46,47

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 Q13007-1_Q13007-1_6df3_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 Q13007-1_6df3_C_Q13007-2.pdb

3D view using mol* of Q13007-1_6df3_C_Q13007-3.pdb

3D view using mol* of Q13007-1_6df3_C_Q13007-4.pdb

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

3D view using mol* of Q13007-1_Q13007-2.pdb

3D view using mol* of Q13007-1_Q13007-3.pdb

3D view using mol* of Q13007-1_Q13007-4.pdb

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

./stats/secondary_structure/figure/Q13007-1_vs_Q13007-2.png

./stats/secondary_structure/figure/Q13007-1_vs_Q13007-3.png

./stats/secondary_structure/figure/Q13007-1_vs_Q13007-4.png

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

./stats/relative_asa/Q13007-1_vs_Q13007-2.png

./stats/relative_asa/Q13007-1_vs_Q13007-3.png

./stats/relative_asa/Q13007-1_vs_Q13007-4.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 IL24

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to IL24

Previous studies relating to the alternative splicing of IL24 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in IL24

(ClinVar, 04/20/2024)

accession_id	uniprot_id	gene_name	Type	Variant	Clinical_significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Leu180Val	Benign
Q13007	Q13007-1	IL24	single nucleotide variant	p.Leu180Val	Benign
Q13007	Q13007-1	IL24	single nucleotide variant	p.Leu10Pro	Benign
Q13007	Q13007-1	IL24	single nucleotide variant	p.Leu10Pro	Benign
Q13007	Q13007-1	IL24	single nucleotide variant	p.Ser88Arg	Uncertain significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Ser88Arg	Uncertain significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Thr198Ile	Uncertain significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Thr198Ile	Uncertain significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Glu158Lys	Uncertain significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Glu158Lys	Uncertain significance
Q13007	Q13007-1	IL24	single nucleotide variant	p.Tyr124His	Benign
Q13007	Q13007-1	IL24	single nucleotide variant	p.Tyr124His	Benign