KAIKOcDNA

2014/10/20

Web 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
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. EST Table
  3. Cluster Table
  4. ORF Table
  5. InterProScan Result
  6. cDNA library Table
Return to Top

2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "KAIKOcDNA" data.
File README_e.html(English)
Return to Top

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 itemDescription
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
Return to Top

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 itemDescription
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)
Return to Top

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 itemDescription
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
Return to Top

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 itemDescription
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
Return to Top

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 itemDescription
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
Return to Top

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.

Creative Commons License

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:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. 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:

  1. 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.
  2. You must distribute any derivative work based on part or whole of the data from this database under the license.
  3. 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

Return to Top

4. Update History

DateUpdate 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.
Return to Top

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

Return to Top