Search proteins (genes) in IRView

Search Proteins/Genes

IRView can be searched by protein (or gene) names, gene symbols (including alias names), NCBI Entrez GeneIDs, RefSeq IDs, species names, or free keywords (e.g., 'AP-1', 'Human' and 'transcription factor'). Free keyword searches are applied against RefSeqIDs, GeneSymbols, Synonyms, Gene names (including those of interactants), and Species names, and only RefSeqIDs, Gene symbols, and Species names are listed in the result page. Therefore, if you cannot find specified word(s) in the result list, it means that the specified word(s) corrsponds to one of these excluded fields (i.e., Synonyms, Gene names or those of interactants) in individual [Region information] pages. Although free keyword search is a simple and useful method, sometimes the obtained results list is too large to check individually. In such cases, users can narrow the search range using the following field specifiers and/or logical operators.

Field specifier search

IRView supports several field specifiers to limit the scope of searches. When a query is executed without any field specifiers, all entries whose protein (or gene) names, gene symbols (including alias names), NCBI Entrez GeneIDs, RefSeq IDs or species names match the query expression will be returned.

Field Sample queries
gene gene:"transcription factor"
gene.id gene.id:3725
gene.symbol gene.symbol:jun
refseq refseq:NP_000193.1
origin origin:human

Logical operators

You can use logical operators to join two expressions within a query. AND, OR and NOT are supported in this database.

Logical Operator Sample queries
AND (default) gene.symbol:fos AND origin:human
OR gene.id:2353 OR gene.id:3725
NOT gene.symbol:fos NOT gene.symbol:fosl
Combination (fos AND jun) AND origin:(human OR mouse)

Query results

Query results screen

The above figure is a sample of query results. You can select RefSeq IDs of interest from the results and go to the [Region information] page by clicking on those IDs. Query results can be sorted in ascending or descending order of RefSeq ID, Gene symbol, Origin or number of IRs (indicated by red rectangle) overlapping with other annotated regions (See also [Region information] page - [Interacting regions]) by clicking on the column headers.

[Region information] pages

Representative and other related sequences

Each [Region information] page corresponds to NCBI RefSeq sequences (e.g., NP_005243.1). Longest RefSeq sequences among isoforms derived from the same genes are used as a [Representative sequence] in the database. A [Gene summary] section contains gene name, symbol(s), GeneID and organism for representative RefSeq sequences. Positional information of sequences other than representative ones are displayed in the [Related sequences] section.

Domain/Motif regions

Positions of known conserved domains and motifs obtained from InterPro are displayed in the [Domain/Motif regions] section.

Toggle bars

You can hide particular areas within the [Region information] page by clicking title bars indicated by red solid trizngles. If you click again, hidden areas will appear.

Hiding bars

Sorting of Columns

You can sort columns by clicking on column headers indicated by red circles above.

Sorting regions

Structured regions and mapping

You can map regions of interest to the 3D structure when the structure data of its region is available.

  1. Select PDB structure from ratio buttons indicated by a blue rectangle
  2. Select the region(s) to map from by checking boxes indicated by a red rectangle

Mapping PDB

Variant regions

Variant regions were divided into the following three categories based on results of pair-wise alignment by ClustalW between representative RefSeq and each related sequence.

Types of variant regions Definitions
missing in refseq sequence A missing >5 a.a. region in representative refseq sequence except for end gaps.
missing in related sequence A missing >5 a.a. region in related sequence except for end gaps.
mutually exclusive Mutually exclusive regions (>5 a.a.) between representative refseq and related sequence.

Non-synonymous SNPs

Data on non-synonymous SNPs that potentially affect protein interactions were obtained from the dbSNP web site. You can see detailed information on each of the non-synonymous SNPs in the dbSNP site.

Interacting regions

Regions that interact with other proteins specified in the [Interactants] column are displayed with references in this section. At this time, IRView stores interaction region data that were determined by the in vitro virus (IVV) method (Miyamoto-Sato et al., Nucleic Acids Res. 2004, 32(21):e169.) and the yeast two-hybrid system. The [# of rec] column refers to the number of identical regions recorded in the database. Icons in the [Relation] column stores information on overlapping with annotated regions.

Icons Explanations
Domain/Motif icon An interaction region overlaps with Domain/Motif regions
non-synonymous SNPs icon An interaction region overlaps Information on overlapping with non-synonymous SNPs regions
Structured icon An interaction region overlaps with structured regions
Variant icon An interaction region overlaps with variant regions
Interacting icon An interaction region overlaps with region(s) determined as an interaction region for different protein(s)

Contacting amino acids (calculated from 3D structures)

Contacting amino acids in complex structures are displayed as positions in the representative RefSeq sequence. Proteins that interact with those amino acids are displayed in the [Interactants] column. We defined contacting amino acids as those having atoms within 4.0Å of the other protein. Icons in the [Relation] column stores information on overlapping with specific regions.

Custom regions

IRView allows users to compare positional relationships between arbitral IRs (e.g., in-house data) and pre-included IRs by inputting IR positions to the form box in the [Add custom regions] section.

Contact Information

Contact persons

*corresponding author
MIYAMOTO-SATO, Etsuko*