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:IRF7

Protein Summary

Gene summary

Gene name: IRF7
ASpdb.0 ID: 3665
	Gene
Gene symbol	IRF7
Gene ID	3665
Gene name	interferon regulatory factor 7
Synonyms	IMD39\|IRF-7\|IRF-7H\|IRF7A\|IRF7B\|IRF7C\|IRF7H
Cytomap	11p15.5
Type of gene	protein-coding
Description	interferon regulatory factor 7interferon regulatory factor-7H
Modification date	20240403
UniProtAcc	Q92985

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	IRF7	GO:0000785	chromatin	11473119
Gene	IRF7	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	17404045
Gene	IRF7	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	17404045
Gene	IRF7	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	21931555
Gene	IRF7	GO:0002819	regulation of adaptive immune response	17404045
Gene	IRF7	GO:0005634	nucleus	22065573
Gene	IRF7	GO:0005654	nucleoplasm	-
Gene	IRF7	GO:0005737	cytoplasm	19176627
Gene	IRF7	GO:0005829	cytosol	-
Gene	IRF7	GO:0032481	positive regulation of type I interferon production	17404045
Gene	IRF7	GO:0032727	positive regulation of interferon-alpha production	16127453
Gene	IRF7	GO:0045944	positive regulation of transcription by RNA polymerase II	16127453\|17404045
Gene	IRF7	GO:0051607	defense response to virus	21478870
Gene	IRF7	GO:1990837	sequence-specific double-stranded DNA binding	28473536

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
Q92985-1	Q92985-1_2o61_A.pdb	2O61	X-ray	2.8	A	20	125

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

Q92985

IRF7

Q92985-1

Q92985-2

503

474

228

256

Deletion

none

227

Q92985

IRF7

Q92985-1

Q92985-3

503

164

152

164

Substitution

GGPPGPFLAHTHA

AQGSLLGSCTGGQ

152

164

Q92985

IRF7

Q92985-1

Q92985-3

503

164

165

503

Deletion

none

164

Q92985

IRF7

Q92985-1

Q92985-4

503

516

Substitution

MALAPE

MPVPERPAAGPDSPRPGTR

Multiple sequence alignment of our canonical and alternatively spliced IRF7

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of IRF7

UniProt-id	ENSG	ENST	ENSP
Q92985-1	ENSG00000185507.21	ENST00000525445.6	ENSP00000434009.2
Q92985-1	ENSG00000276561.4	ENST00000621391.4	ENSP00000480358.1
Q92985-2	ENSG00000185507.21	ENST00000348655.11	ENSP00000331803.9
Q92985-2	ENSG00000276561.4	ENST00000633943.1	ENSP00000488666.1
Q92985-3	ENSG00000185507.21	ENST00000469048.6	ENSP00000434607.1
Q92985-3	ENSG00000185507.21	ENST00000533182.5	ENSP00000433903.1
Q92985-3	ENSG00000276561.4	ENST00000633274.1	ENSP00000488591.1
Q92985-3	ENSG00000276561.4	ENST00000634105.1	ENSP00000488581.1
Q92985-4	ENSG00000185507.21	ENST00000330243.9	ENSP00000329411.5
Q92985-4	ENSG00000185507.21	ENST00000397566.5	ENSP00000380697.1
Q92985-4	ENSG00000276561.4	ENST00000612534.4	ENSP00000479615.1
Q92985-4	ENSG00000276561.4	ENST00000632827.1	ENSP00000488039.1

UniProt-id	NM ID	NP ID
Q92985-1	NM_001572.3	NP_001563.2
Q92985-2	NM_004029.2	NP_004020.1
Q92985-4	NM_004031.2	NP_004022.2

Amino acid sequences of our canonical and alternatively spliced IRF7

accession_id	Protein sequence
Q92985-1	MALAPERAAPRVLFGEWLLGEISSGCYEGLQWLDEARTCFRVPWKHFARKDLSEADARIFKAWAVARGRWPPSSRGGGPPPEAETAERAG WKTNFRCALRSTRRFVMLRDNSGDPADPHKVYALSRELCWREGPGTDQTEAEAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKG DLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAVETTPSPGPQPAALTTGEAAAPESPHQAEPY LSPSPSACTAVQEPSPGALDVTIMYKGRTVLQKVVGHPSCTFLYGPPDPAVRATDPQQVAFPSPAELPDQKQLRYTEELLRHVAPGLHLE LRGPQLWARRMGKCKVYWEVGGPPGSASPSTPACLLPRNCDTPIFDFRVFFQELVEFRARQRRGSPRYTIYLGFGQDLSAGRPKEKSLVL
Q92985-2	MALAPERAAPRVLFGEWLLGEISSGCYEGLQWLDEARTCFRVPWKHFARKDLSEADARIFKAWAVARGRWPPSSRGGGPPPEAETAERAG WKTNFRCALRSTRRFVMLRDNSGDPADPHKVYALSRELCWREGPGTDQTEAEAPAAVPPPQGGPPGPFLAHTHAGLQAPGPLPAPAGDKG DLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGEAAAPESPHQAEPYLSPSPSACTAVQEPSPGALDVTIMYKGRT VLQKVVGHPSCTFLYGPPDPAVRATDPQQVAFPSPAELPDQKQLRYTEELLRHVAPGLHLELRGPQLWARRMGKCKVYWEVGGPPGSASP STPACLLPRNCDTPIFDFRVFFQELVEFRARQRRGSPRYTIYLGFGQDLSAGRPKEKSLVLVKLEPWLCRVHLEGTQREGVSSLDSSSLS
Q92985-3	MALAPERAAPRVLFGEWLLGEISSGCYEGLQWLDEARTCFRVPWKHFARKDLSEADARIFKAWAVARGRWPPSSRGGGPPPEAETAERAG
Q92985-4	MPVPERPAAGPDSPRPGTRRAAPRVLFGEWLLGEISSGCYEGLQWLDEARTCFRVPWKHFARKDLSEADARIFKAWAVARGRWPPSSRGG GPPPEAETAERAGWKTNFRCALRSTRRFVMLRDNSGDPADPHKVYALSRELCWREGPGTDQTEAEAPAAVPPPQGGPPGPFLAHTHAGLQ APGPLPAPAGDKGDLLLQAVQQSCLADHLLTASWGADPVPTKAPGEGQEGLPLTGACAGGPGLPAGELYGWAVETTPSPGPQPAALTTGE AAAPESPHQAEPYLSPSPSACTAVQEPSPGALDVTIMYKGRTVLQKVVGHPSCTFLYGPPDPAVRATDPQQVAFPSPAELPDQKQLRYTE ELLRHVAPGLHLELRGPQLWARRMGKCKVYWEVGGPPGSASPSTPACLLPRNCDTPIFDFRVFFQELVEFRARQRRGSPRYTIYLGFGQD

Protein Functional Features

Main function of this protein. (from UniProt)

IRF7 (go to UniProt):Q92985

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
Q92985	Region	133	156	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=152;End=164
Q92985	Region	242	277	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=228;End=256
Q92985	Region	242	277	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=165;End=503
Q92985	Region	284	456	Note=Necessary for the interaction with NMI;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P70434	Type=Deletion;Start=165;End=503

Gene Isoform Structures and Expression Levels for IRF7

Gene structures of our canonical and alternative spliced genes of IRF7
* 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 Q92985-1

3D view using mol* of Q92985-2

3D view using mol* of Q92985-3

3D view using mol* of Q92985-4

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 Q92985-1

pLDDT distribution across the protein length of Q92985-2

pLDDT distribution across the protein length of Q92985-3

pLDDT distribution across the protein length of Q92985-4

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 Q92985-1

Ramachandran plot of Q92985-3

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
Q92985-1	1.04	139	1.093	460.306	0.594	0.687	0.856	0.905	0.793	1.141	1.56	283,286,418,456,457,459,460,461,463,464,465,467,46 8,471,475,477,478,480,481,482,483,484,485,487,488, 491,494,495,498
Q92985-2	1.042	159	1.07	623.574	0.535	0.738	1.006	0.922	0.961	0.959	0.686	15,19,102,103,104,124,127,128,129,130,131,132,182, 185,186,189,190,335,336,349,350,351,362,363,365,37 3,374,375,376,377,379,380,381,382,383,384,386,397, 398
Q92985-3	0.792	55	0.711	133.77	0.574	0.67	0.948	0.091	1.189	0.076	0.728	27,28,29,41,43,44,45,47,55,56,58,59,60,116,117,118 ,119
Q92985-4	0.953	349	0.915	829.717	0.619	0.628	0.846	0.167	1.231	0.136	0.908	21,22,23,24,25,26,27,28,32,36,45,49,50,51,52,76,78 ,79,80,81,82,111,114,115,117,119,136,137,138,139,1 40,141,142,143,144,145,146,390,392,394,395,396,397 ,398,399,401,402,403,404,405,406,407,408,430,433,4 34,435,436,440,444,450,451,452,453,454,455,456,457 ,458,482,483,484,485,486,487

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 Q92985-1_Q92985-1_2o61_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 Q92985-1_2o61_A_Q92985-2.pdb

3D view using mol* of Q92985-1_2o61_A_Q92985-3.pdb

3D view using mol* of Q92985-1_2o61_A_Q92985-4.pdb

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

3D view using mol* of Q92985-1_Q92985-2.pdb

3D view using mol* of Q92985-1_Q92985-3.pdb

3D view using mol* of Q92985-1_Q92985-4.pdb

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

./stats/secondary_structure/figure/Q92985-1_vs_Q92985-2.png

./stats/secondary_structure/figure/Q92985-1_vs_Q92985-3.png

./stats/secondary_structure/figure/Q92985-1_vs_Q92985-4.png

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

./stats/relative_asa/Q92985-1_vs_Q92985-2.png

./stats/relative_asa/Q92985-1_vs_Q92985-3.png

./stats/relative_asa/Q92985-1_vs_Q92985-4.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q92985	Region	284	456	Note=Necessary for the interaction with NMI;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P70434	Type=Deletion;Start=165;End=503

Interactors from STRING.

Gene name

Interactors

Related Drugs to IRF7

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to IRF7

Previous studies relating to the alternative splicing of IRF7 and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
IRF7	20209099	Dual functions of interferon regulatory factors 7C in Epstein-Barr virus-mediated transformation of human B lymphocytes.	Epstein-Barr virus (EBV) infection is associated with several human malignancies. Interferon (IFN) regulatory factor 7 (IRF-7) has several splicing variants, and at least the major splicing variant (IRF-7A) has oncogenic potential and is associated with EBV transformation processes. IRF-7C is an alternative splicing variant with only the DNA-binding domain of IRF-7. Whether IRF-7C is present under physiological conditions and its functions in viral transformation are unknown. In this report, we prove the existence of IRF-7C protein and RNA in certain cells under physiological conditions, and find that high levels of IRF-7C are associated with EBV transformation of human primary B cells in vitro as well as EBV type III latency. EBV latent membrane protein 1 (LMP-1) stimulates IRF-7C expression in B lymphocytes. IRF-7C has oncogenic potential in rodent cells and partially restores the growth properties of EBV-transformed cells under a growth-inhibition condition. A tumor array experiment has identified six primary tumor specimens with high levels of IRF-7C protein--all of them are lymphomas. Furthermore, we show that the expression of IRF-7C is apparently closely associated with other IRF-7 splicing variants. IRF-7C inhibits the function of IRF-7 in transcriptional regulation of IFN genes. These data suggest that EBV may use splicing variants of IRF-7 for its transformation process in two strategies: to use oncogenic properties of various IRF-7 splicing variants, but use one of its splicing variants (IRF-7C) to block the IFN-induction function of IRF-7 that is detrimental for viral transformation. The work provides a novel relation of host/virus interactions, and has expanded our knowledge about IRFs in EBV transformation.	D002472	Cell Transformation, Viral

Clinically important variants in IRF7

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance