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Protocols

SilkBase specifications

Information


Unique identifier OMICS_22521
Name SilkBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Bombyx mori

Maintainer


  • person_outline Marian Goldsmith

Publication for SilkBase

SilkBase citations

 (8)
library_books

The biogenesis pathway of tRNA derived piRNAs in Bombyx germ cells

2017
Nucleic Acids Res
PMCID: 5587776
PMID: 28645172
DOI: 10.1093/nar/gkx537

[…] From SilkBase (http://silkbase.ab.a.u-tokyo.ac.jp/cgi-bin/index.cgi), we retrieved the BGIBMGA002973-TA and BGIBMGA004408-TA GeneModel sequences as significant homologs to human THG1L (NP_060342.2) and NSU […]

call_split

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses

2015
PLoS Genet
PMCID: 4574769
PMID: 26379286
DOI: 10.1371/journal.pgen.1005470
call_split See protocol

[…] The putative ORFs were determined with the EditSeq program from DNASTAR and the homologs in other insect species were obtained using BLAST comparison at NCBI (http://www.ncbi.nlm.nhi.gov), Silkbase (http://silkworm.genomics.org.cn), Manduca sexta genome project (http://agripestbase.org/manduca) and LepidoDB (http://www6.inra.fr/lepidodb). The predicted amino acid sequences were aligned […]

call_split

Glutathione Binding Site of a Bombyx mori Theta Class Glutathione Transferase

2014
PLoS One
PMCID: 4029803
PMID: 24848539
DOI: 10.1371/journal.pone.0097740
call_split See protocol

[…] NA was used as a PCR template with the oligonucleotide primers 5′-TATACCATGGTTTTAAAACTATATTATGAT-3′ (sense) and 5′-CCGGATCCTTAAAGTTTAGAATTAGCCGCA-3′ (antisense), based on a sequence obtained from the SilkBase EST database . Underlined and double-underlined regions in the primer sequences represent NcoI and BamHI restriction enzyme sites, respectively, which were used to insert the PCR product into […]

library_books

Molecular Evidence of RNA Editing in Bombyx Chemosensory Protein Family

2014
PLoS One
PMCID: 3923736
PMID: 24551045
DOI: 10.1371/journal.pone.0086932

[…] morCSP1, BmorCSP2, BmorCSP4 and BmorCSP14 were all found in the scaffold 36 (contigs BABH01021425, BABH01021427, BABH01021421 and BABH01021426, respectively). Similar analysis was performed using the SilkBase at http://www.silkdb.org/silkdb/ , . In the SilkBase, BmorCSP1, BmorCSP4 and BmorCSP14 genomic sequences were found in the scaffold nscaf2767 (contigs BGIBMGA004068-TA, BGIBMGA004047-TA and B […]

library_books

Transcriptome Analysis in Cotton Boll Weevil (Anthonomus grandis) and RNA Interference in Insect Pests

2013
PLoS One
PMCID: 3874031
PMID: 24386449
DOI: 10.1371/journal.pone.0085079

[…] icant and representative portion of the A. grandis transcriptome. We performed a comparison of the A. grandis 454 Pfam entries to D. melanogaster and B. mori Pfam transcript sects from Flybase [] and Silkbase [] (with tBLASTx, e < 10-3) in order to establish a simplified genetic overlap between these species. The low number of A. grandis sequences, which do not match either D. melanogaster or B. m […]

library_books

Molecular Analysis of the Muscle Protein Projectin in Lepidoptera

2013
PMCID: 3835035
PMID: 24206568
DOI: 10.1673/031.013.8801

[…] sequence to the 6-frame-translation of a DNA sequence; in this case, the contigs available for the B. mori genome (). The EST database from the two silkworm transcriptome projects, available through SILKBASE and GenBank, was also searched, and resulting EST sequences were aligned on the genomic sequence. For the D. plexippus projectin, a BLAST search of the recently published genome was performed […]

Citations

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SilkBase institution(s)
Laboratory of Insect Genome, National Institute of Agrobiological Sciences, Ibaraki, Japan; National Institute of Radiological Sciences, Chiba, Japan; Laboratory of Molecular Entomology and Baculovirology, The Institute of Physical and Chemical Research (RIKEN), Saitama, Japan; Department of Agricultural and Environmental Biology, University of Tokyo, Tokyo, Japan; Faculty of Agriculture, Utsunomiya University, Tochigi, Japan; Biological Sciences Department, University of Rhode Island, Kingston, RI, USA
SilkBase funding source(s)
Supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences and the Animal Genome Research Program in the Ministry of Agriculture, Forestry, and Fisheries of Japan; in part by Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research 13202074 and 15011207; and The Japan Society for the Promotion of Science ‘‘Research for the Future’’ Program Life Science Grant 12-1.

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