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KAIKObase specifications


Unique identifier OMICS_05800
Name KAIKObase
Restrictions to use None
Maintained Yes


  • Invertebrates
    • Bombyx mori


  • person_outline Kimiko Yamamoto

Publication for KAIKObase

KAIKObase citations


Conservation and lineage specific rearrangements in the GOBP/PBP gene complex of distantly related ditrysian Lepidoptera

PLoS One
PMCID: 5806886
PMID: 29425254
DOI: 10.1371/journal.pone.0192762

[…] ion was derived from an allele existing in the colony used for the BAC library construction.We then searched for conserved CDS in 25F18 and 28N16 inserts by TBLASTX against a B. mori genome database, Kaikobase. We found an incomplete CDS (named tentatively CDS-A) located approximately 5 kb upstream of the OnubGOBP2 gene (). CDS-A was similar to exon1 of a B. mori gene model, BGIBMGA012613, located […]


Genome Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori

Int J Mol Sci
PMCID: 5855749
PMID: 29425159
DOI: 10.3390/ijms19020527

[…] elegans, Onchocerca volvulus, Brugia malayi, Pristionchus pacificus and Strongyloides ratti.The chromosomal locations, gene lengths, probes and predicted protein lengths were obtained from SilkDB and KAIKObase. Theoretical molecular weights and isoelectric point values were calculated online at http://web.expasy.org/protparam/. Three online programs, CDD (http://www.ncbi.nlm.nih.gov/Structure/cdd/ […]


The pivotal role of aristaless in development and evolution of diverse antennal morphologies in moths and butterflies

BMC Evol Biol
PMCID: 5785806
PMID: 29370752
DOI: 10.1186/s12862-018-1124-2

[…] under a stereomicroscope or a compound microscope.We also tried to knock down al function by RNAi. There are at least two al homologs in the B. mori genome (al1/BMgn006008 and al2/BMgn006007, SilkDB/KAIKObase). We designed four different siRNAs for each of al1 and al2, and used them in various combinations. However, we failed to deplete either of al1 or al2 mRNA effectively by unknown reason (dat […]


Genome wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

Sci Rep
PMCID: 5635003
PMID: 29018289
DOI: 10.1038/s41598-017-13186-6
call_split See protocol

[…] b.org/silkdb/doc/download.htm) using bowtie2 software (Version 2.2.9). Low-quality reads were removed using Trimmomatic (Table ). The cleaned short reads were mapped to the silkworm reference genome (KAIKObase) with TopHat (Version 2.0.12.). Differentially expressed genes (DEGs) were detected using Cuffdiff and RSEM (Version 1.2.29). We defined the intersects of the DEGs generated by these two sof […]


RNA sequencing reveals a complete but an unconventional type of dosage compensation in the domestic silkworm Bombyx mori

R Soc Open Sci
PMCID: 5541547
PMID: 28791152
DOI: 10.1098/rsos.170261

[…] is required for current analysis. So, to overcome this, the ‘description’ code of each gene in the GFF file was replaced with its corresponding chromosome number, based on the scaffold identity from KAIKObase [] annotation data using custom shell scripts. […]


Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands

Sci Data
PMCID: 5004587
PMID: 27576083
DOI: 10.1038/sdata.2016.73

[…] hit in the NCBI Primer-BLAST webpage (http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome) using the RefseqmRNA database and Bombyx mori as the organism, 4) unique hit in the KAIKObase website using Blastn. […]


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KAIKObase institution(s)
Mitsubishi Space Software Co Ltd, Takezono, Tsukuba, Ibaraki, Japan

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