ASTRA
2015/11/25Web Site: -
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/astra/
The database represents classified patterns of alternative splicing (AS) and alternative transcriptional initiation (ATI) in six eukaryotic genomes.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "ASTRA" data. |
| File | README_e.html(English) |
2.2 Locus
| Data name | Locus |
| Description of data contents | List of locus and splicing patterns in respective locus |
| File | astra_locus.zip (887 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Locus ID | Specific locus ID for this database |
| UniGene ID | UniGene ID |
| Species | Species name |
| Chr. No. | Chromosome No. |
| Strand | Strand |
| Matched genome | Definition of the genome sequence matching this locus |
| Matched genome (GI) | Genbank ID of the genome sequence matching this locus |
| Matched genome (RefSeq) | RefSeq ID of the genome sequence matching this locus |
| Gene name | Gene name |
| Left | The left position of this locus onto genome |
| Right | The right position of this locus onto genome |
| GO | Gene Ontology |
| Variants | Number of splicing variants |
| Splicing type | Splicing type (ex. cassette) |
2.3 cDNA
| Data name | cDNA |
| Description of data contents | List of cDNA in locus |
| File | astra_cdna.zip (3.3 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| cDNA ID | Specific cDNA ID for this database |
| Locus ID | Specific locus ID for this database |
| Species | Species name |
| Chr. No. | Chromosome No. |
| Strand | Strand |
| Gene name | Gene name |
| UniGene ID | UniGene ID |
| cDNA UniGene ID | UniGene ID of this cDNA |
| Genbank accession | Genbank accession number |
| GI | Genbank ID |
| CDS left | The left position of coding region onto this cDNA |
| CDS right | The right position of coding region onto this cDNA |
| Splicing pattern | Splicing pattern (gene model) |
| cDNA sequence length | cDNA sequence length |
| DOU start | Premature (pseudo) start codon (true) or not (false) |
| DOU end | Premature (pseudo) stop codon (true) or not (false) |
| NMD | Nonsense-mediated mRNA Decay (NMD) might happen (true) or not (false) |
| Number of exons | Number of exons in this variant |
| Number of splicing regions | Number of alternative splicing/transcriptional initiation regionss |
2.4 Exon
| Data name | Exon |
| Description of data contents | Exons in variants |
| File | astra_exon.zip (5.9 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Exon ID | Specific exon ID for this database |
| Species | Species name |
| Locus ID | Specific locus ID for this database |
| cDNA ID | Specific cDNA ID for this database |
| Left in cDNA | The left position of exon onto cDNA |
| Right in cDNA | The right position of exon onto cDNA |
| Left in genome | The left position of exon onto genome |
| Right in genome | The right position of exon onto genome |
2.5 Splicing pattern
| Data name | Splicing pattern |
| Description of data contents | The patterns of alternative splicing/transcriptional initiation |
| File | astra_splicing_pattern.zip (1.2 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| ID | ID for splicing pattern |
| Species | Species name |
| Locus ID | Specific locus ID for this database |
| Region | Splicing Region number in this locus |
| Splicing pattern | Splicing pattern number in this locus |
| cDNA ID | Specific cDNA ID for this database |
| Splicing left | The left position of splicing region onto genome |
| Splicing right | The right position of splicing region onto genome |
| Splicing pattern | Splicing pattern represented into bit array. "1" means splicing region. |
| Splicing type | Splicing type (ex. cassette) |
| NAGNAG | NAGNAG (6bp acceptor site) or not |
3. License
Last updated : 2015/11/25
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "ASTRA © Hideki Nagasaki (National Institute of Advanced Industrial Science and Technology) licensed under CC Attribution-Share Alike 4.0 International".
The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other adapted materials based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
- You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
E-mail: nagasaki[at]kazusa[dot]or[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2015/11/25 | ASTRA English archive site is opened. |
| 2005 | ASTRA (http://alterna.cbrc.jp/) is opened. |
5. Literature
Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O.Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.
Gene. 2005 Dec 30;364:53-62.
Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O.
Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.
Bioinformatics. 2006 May 15;22(10):1211-6.
6. Contact address
When you have any question about "ASTRA", contact the following:E-mail: nagasaki[at]kazusa[dot]or[dot]jp