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Protocols

PHYSCObase specifications

Information


Unique identifier OMICS_22418
Name PHYSCObase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Mitsuyasu Hasebe

Additional information


http://moss.nibb.ac.jp/protocol.html

Publication for PHYSCObase

PHYSCObase citations

 (4)
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In Silico and Biochemical Analysis of Physcomitrella patens Photosynthetic Antenna: Identification of Subunits which Evolved upon Land Adaptation

2008
PLoS One
PMCID: 2323573
PMID: 18446222
DOI: 10.1371/journal.pone.0002033
call_split See protocol

[…] Sequence searches were performed in PHYSCObase database (http://moss.nibb.ac.jp/blast/blast.html) that contained 196,310 sequences from clones isolated from three Physcomitrella patens full-length-enriched cDNA libraries , sequenced bot […]

library_books

Evolutionary genomics of plant genes encoding N terminal TM C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

2007
BMC Genomics
PMCID: 1976326
PMID: 17672888
DOI: 10.1186/1471-2164-8-259

[…] d Oryza sativa but both of these represent relatively recently evolved angiosperms whereas the moss genome represents an ancient bryophyte. I used the trace archive at NCBI [] as well as resources at PHYSCObase [] where transcript sequences are also available. I confirmed the genomic and transcript sequences from several Physcomitrella patens gene loci and deposited these sequences in the public d […]

call_split

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins

2006
Nucleic Acids Res
PMCID: 1636356
PMID: 16936312
DOI: 10.1093/nar/gkl570
call_split See protocol

[…] rice SR proteins using ClustalW program () at . Shading of multiple alignment files was done with BOXSHADE at .Contigs were used to retrieve genomic sequences at NCBI and species specific databases (PHYSCObase, ; ChlamyDB ). Genomic sequences were used in screen for additional ESTs representing splice variants. Gene structures and alternative splicing events were finally analysed using Geneseqer. […]

library_books

Genome wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa

2005
BMC Evol Biol
PMCID: 1368998
PMID: 16368012
DOI: 10.1186/1471-2148-5-72

[…] d for subsequent analysis. Sequences encoding putative IQD proteins in Pinus ssp. and Physcomitrella patens were identified by BLAST searches of the TIGR Gene Indices [] and of the moss database NIBB PHYSCObase []. […]

Citations

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PHYSCObase institution(s)
Division of Speciation Mechanisms, Okazaki, Japan; Computer Laboratory, National Institute for Basic Biology, Okazaki, Japan; Genome Biology Laboratory, Center for Genetic Resource Information, National Institute of Genetics, Mishima, Japan; Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba, Japan; Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, Yokohama, Japan; Research Center for Computational Science, Okazaki National Research Institute, Okazaki, Japan; Genome Science Laboratory, RIKEN, Wako, Japan; Department of Molecular Biomechanics, SOKENDAI, Okazaki, Japan
PHYSCObase funding source(s)
Supported by a Grant-in-Aid for Scientific Research on Priority Areas (C) ‘‘Genome Science’’ from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), Grant-in Aid for Scientific Research on Priority Areas (Grants 14036229 and 13044001) from MEXT, a Grant-in-Aid from MEXT, Japan Society for the Promotion of Science (JSPS) Grant RFTF00L0162, Genome Research from RIKEN, the Program for Promotion of Basic Research Activities for Innovative Biosciences, the Special Coordination Fund of the Science and Technology Agency, and a Grant-in-Aid from MEXT.

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