KAIKOcDNA
2014/10/20Web Site: http://sgp.dna.affrc.go.jp/EST/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/kaiko-cdna/
The database of silkworm partial cDNA sequences with annotations.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "KAIKOcDNA" data. |
| File | README_e.html(English) |
2.2 EST Table
| Data name | EST Table |
| Description of data contents | List of silkworm ESTs (cDNAs) consisting of publicly available data in addition to sequences registered to public database as of September 2011. |
| File | kaiko_cdna_main.zip (157 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Accession Number | Accession number of EST |
| Clone Name | Clone name of EST |
| Length | Sequence length (bp) |
| GO check_date | Date of InterProScan run |
| GO Iprscan Value | Link to result of InterProScan |
| GO ID | Assigned GO IDs |
| NR blast_date | Date of BLAST search (DB: NCBI nr) |
| NR value | Result of BLAST search (DB: NCBI nr) |
| NR definition | Definition of homologous sequence (DB: NCBI nr) |
| Drosophila blast_date | Date of BLAST search (DB: D. melanogaster proteins) |
| Drosophila value | Result of BLAST search (DB: D. melanogaster proteins) |
| Drosophila definition | Definition of homologous sequence (DB: D. melanogaster proteins) |
| C.elegans blast_date | Date of BLAST search (DB: C.elegans proteins) |
| C.elegans value | Result of BLAST search (DB: C.elegans proteins) |
| C.elegans definition | Definition of homologous sequence (DB: C.elegans proteins) |
| Anopheles blast_date | Date of BLAST search (DB: A. gambiae proteins) |
| Anopheles value | Result of BLAST search (DB: A. gambiae proteins) |
| Anopheles definition | Definition of homologous sequence (DB: Anopheles) |
| Apis blast_date | Date of BLAST search (DB: A. mellifera proteins) |
| Apis value | Result of BLAST search (DB: A. mellifera proteins) |
| Apis definition | Definition of homologous sequence (DB: A. mellifera proteins) |
| Tribolium blast_date | Date of BLAST search (DB: T. castaneum proteins) |
| Tribolium value | Result of BLAST search (DB: T. castaneum proteins) |
| Tribolium definition | Definition of homologous sequence (DB: T. castaneum proteins) |
| Cluster Size | Number of sequences in cluster |
| Rep ID | Accession number of the representative sequence |
| cDNA library name | cDNA library name |
| Sequence | Sequence |
2.3 Cluster Table
| Data name | Cluster Table |
| Description of data contents | List of number of identical cDNA sequences that make up cluster. |
| File | kaiko_cdna_cluster.zip (453 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Rep ID | Accession number of the representative EST of each cluster |
| Cluster Size | Number of total clones in each cluster |
| an-- | Number of identical clones (cDNA library an--) |
| bmmt | Number of identical clones (cDNA library bmmt) |
| bmov | Number of identical clones (cDNA library bmov) |
| bmte | Number of identical clones (cDNA library bmte) |
| BmN- | Number of identical clones (cDNA library BmN-) |
| br-- | Number of identical clones (cDNA library br--) |
| brP- | Number of identical clones (cDNA library brP-) |
| brS- | Number of identical clones (cDNA library brS-) |
| caL- | Number of identical clones (cDNA library caL-) |
| ce-- | Number of identical clones (cDNA library ce--) |
| ceN- | Number of identical clones (cDNA library ceN-) |
| cesb | Number of identical clones (cDNA library cesb) |
| dpe- | Number of identical clones (cDNA library dpe-) |
| e100 | Number of identical clones (cDNA library e100) |
| e4 | Number of identical clones (cDNA library e4) |
| e96h | Number of identical clones (cDNA library e96h) |
| epM- | Number of identical clones (cDNA library epM-) |
| epV3 | Number of identical clones (cDNA library epV3) |
| F1mg | Number of identical clones (cDNA library F1mg) |
| famL | Number of identical clones (cDNA library famL) |
| fbf | Number of identical clones (cDNA library fbf) |
| fbm | Number of identical clones (cDNA library fbm) |
| fbpv | Number of identical clones (cDNA library fbpv) |
| fbS2 | Number of identical clones (cDNA library fbS2) |
| fcaL | Number of identical clones (cDNA library fcaL) |
| fcP8 | Number of identical clones (cDNA library fcP8) |
| fe8d | Number of identical clones (cDNA library fe8d) |
| ffbm | Number of identical clones (cDNA library ffbm) |
| FJsb | Number of identical clones (cDNA library FJsb) |
| fmgV | Number of identical clones (cDNA library fmgV) |
| fner | Number of identical clones (cDNA library fner) |
| ftes | Number of identical clones (cDNA library ftes) |
| fufe | Number of identical clones (cDNA library fufe) |
| fwgP | Number of identical clones (cDNA library fwgP) |
| heS0 | Number of identical clones (cDNA library heS0) |
| heS3 | Number of identical clones (cDNA library heS3) |
| J150 | Number of identical clones (cDNA library J150) |
| JFsb | Number of identical clones (cDNA library JFsb) |
| maV3 | Number of identical clones (cDNA library maV3) |
| MFB- | Number of identical clones (cDNA library MFB-) |
| mg | Number of identical clones (cDNA library mg) |
| msgV | Number of identical clones (cDNA library msgV) |
| MSV3 | Number of identical clones (cDNA library MSV3) |
| mxg- | Number of identical clones (cDNA library mxg-) |
| n | Number of identical clones (cDNA library n) |
| Nnor | Number of identical clones (cDNA library Nnor) |
| NRPG | Number of identical clones (cDNA library NRPG) |
| NV02 | Number of identical clones (cDNA library NV02) |
| NV06 | Number of identical clones (cDNA library NV06) |
| NV12 | Number of identical clones (cDNA library NV12) |
| ovS0 | Number of identical clones (cDNA library ovS0) |
| ovS3 | Number of identical clones (cDNA library ovS3) |
| P5PG | Number of identical clones (cDNA library P5PG) |
| pg-- | Number of identical clones (cDNA library pg--) |
| phe- | Number of identical clones (cDNA library phe-) |
| prgv | Number of identical clones (cDNA library prgv) |
| prW- | Number of identical clones (cDNA library prW-) |
| ps4M | Number of identical clones (cDNA library ps4M) |
| psV3 | Number of identical clones (cDNA library psV3) |
| PSV3 | Number of identical clones (cDNA library PSV3) |
| tesS | Number of identical clones (cDNA library tesS) |
| tesV | Number of identical clones (cDNA library tesV) |
| vg4M | Number of identical clones (cDNA library vg4M) |
| wd-- | Number of identical clones (cDNA library wd--) |
| wdV1 | Number of identical clones (cDNA library wdV1) |
| wdV3 | Number of identical clones (cDNA library wdV3) |
| ws0 | Number of identical clones (cDNA library ws0) |
| ws2 | Number of identical clones (cDNA library ws2) |
| ws3 | Number of identical clones (cDNA library ws3) |
| wv4 | Number of identical clones (cDNA library wv4) |
| swa | Number of identical clones (cDNA library swa) |
| swb | Number of identical clones (cDNA library swb) |
| swc | Number of identical clones (cDNA library swc) |
| swd | Number of identical clones (cDNA library swd) |
| swe | Number of identical clones (cDNA library swe) |
| swf | Number of identical clones (cDNA library swf) |
| swg | Number of identical clones (cDNA library swg) |
| swh | Number of identical clones (cDNA library swh) |
| swj | Number of identical clones (cDNA library swj) |
| swk | Number of identical clones (cDNA library swk) |
| swl | Number of identical clones (cDNA library swl) |
| swp | Number of identical clones (cDNA library swp) |
| BmP | Number of identical clones (cDNA library BmP) |
| L1 | Number of identical clones (cDNA library L1) |
| L2 | Number of identical clones (cDNA library L2) |
| L3 | Number of identical clones (cDNA library L3) |
| L4 | Number of identical clones (cDNA library L4) |
| L5 | Number of identical clones (cDNA library L5) |
| L6 | Number of identical clones (cDNA library L6) |
| L7 | Number of identical clones (cDNA library L7) |
| L8 | Number of identical clones (cDNA library L8) |
| L9 | Number of identical clones (cDNA library L9) |
| L10 | Number of identical clones (cDNA library L10) |
| L11 | Number of identical clones (cDNA library L11) |
| L12 | Number of identical clones (cDNA library L12) |
| L13 | Number of identical clones (cDNA library L13) |
| L14 | Number of identical clones (cDNA library L14) |
| L15 | Number of identical clones (cDNA library L15) |
| L16 | Number of identical clones (cDNA library L16) |
| Other | Number of identical clones (other cDNA libraries) |
2.4 ORF Table
| Data name | ORF Table |
| Description of data contents | List of open reading frames of the representative ESTs. |
| File | kaiko_cdna_orf.zip (11 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Rep ID | Accession number of the representative EST |
| ORF Name | Name of ORF |
| Frame | Number of Frame |
| ORF Number | Number of ORF |
| Threshold | Threshold of sequence length (including the stop codon) |
| Length | Sequence length (bp) |
| Sequence | Amino acid Sequence |
2.5 InterProScan Result
| Data name | InterProScan Result |
| Description of data contents | List of the result of InterProScan target the representative EST. |
| File | kaiko_cdna_interpro.zip (3.1 MB) |
Data items are the following:
| Data item | Description |
|---|---|
| Rep ID | Accession number of the representative EST |
| ORF Name | Name of ORF |
| CRC64 | Value of CRC64 in each sequence |
| Length | Sequence length (bp) |
| Analysis | Database/Program used for analysis |
| Signature Accession | Signature accession |
| Signature Description | Signature description |
| Start location | Start location of Motif |
| Stop location | Stop location of Motif |
| Score | E-value of matching score to the functional site sequence |
| Status | Status of match to the functional site sequence (T: match) |
| InterPro accession | Assigned InterPro ID |
| InterPro description | Description of assigned InterPro ID |
| GO terms | Assigned GO terms |
2.6 cDNA library Table
| Data name | cDNA library Table |
| Description of data contents | List of Bombyx mori cDNA libraries. |
| File | kaiko_cdna_library.zip (4.8 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Registered library name | Registered name of the partial cDNA library |
| Library synonym | Another name for cDNA library (original name) |
| Local library name | Local library name |
| Strain/Race | Strain/race |
| Organ/Tissue | Organ / tissue |
| Developmental stage | Developmental stage |
| Sex | Sex |
| Vector | Vector |
| Cloning sites | Cloning site |
| Sequence direction | Direction of sequencing |
| Accession number | Range of accession numbers |
| Clone name | Naming rule of clones |
| Note | Note |
3. License
Last updated : 2014/10/08
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 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "KAIKOcDNA © Yoshitaka Suetsugu (National Institute of Agrobiological Sciences) licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan 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 derivative works 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 derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- 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.
Akiya Jouraku
National Institute of Agrobiological Sciences
1-2 Oowashi Tsukuba, Ibaraki 305-8634, Japan
E-mail: joraku[at]affrc[dot]go[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2014/10/20 | The URL of the database maintenance site is changed. |
| 2014/10/08 | KAIKOcDNA English archive site is opened. |
| 2004/04/12 | KAIKOcDNA database (http://sgp.dna.affrc.go.jp/EST/) is opened. |
5. Literature
Suetsugu Y, Futahashi R, Kanamori H, Kadono-Okuda K, Sasanuma S, Narukawa J,Ajimura M, Jouraku A, Namiki N, Shimomura M, Sezutsu H, Osanai-Futahashi M, Suzuki MG, Daimon T, Shinoda T, Taniai K, Asaoka K, Niwa R, Kawaoka S, Katsuma S,Tamura T, Noda H, Kasahara M, Sugano S, Suzuki Y, Fujiwara H, Kataoka H, Arunkumar KP, Tomar A, Nagaraju J, Goldsmith MR, Feng Q, Xia Q, Yamamoto K, Shimada T, Mita K.Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.
G3 (Bethesda) / 2013, Sep / vol.9
PMID: 23821615
6. Contact address
When you have any question about "KAIKOcDNA", contact the following:1-2 Oowashi Tsukuba, Ibaraki 305-8634, Japan
National Institute of Agrobiological Sciences
Akiya Jouraku
E-mail: joraku[at]affrc[dot]go[dot]jp