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Ghost Database specifications

Information


Unique identifier OMICS_22462
Name Ghost Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Yutaka Satou

Publication for Ghost Database

Ghost Database citations

 (5)
call_split

piRNA like small RNAs are responsible for the maternal specific knockdown in the ascidian Ciona intestinalis Type A

2018
Sci Rep
PMCID: 5897368
PMID: 29651003
DOI: 10.1038/s41598-018-24319-w
call_split See protocol

[…] ence sequences. The reference sequences were constructed by combining all of the plasmid sequences used for recombination and the C. intestinalis genome (KH, ver. 2008), which was downloaded from the Ghost Database. The reads per megareads (RPM) value of each nucleotide in reference sequences was calculated by dividing the number of mapped reads (depth) for each nucleotide in the reference sequenc […]

library_books

CiAPEX2 and CiP0, candidates of AP endonucleases in Ciona intestinalis, have 3′ 5′ exonuclease activity and contribute to protection against oxidative stress

2017
PMCID: 5709841
PMID: 29213341
DOI: 10.1186/s41021-017-0087-7

[…] the differences of the roles and functions among AP endonucleases, we focused on the homologues of APEX2 (CiAPEX2) and P0 (CiP0) in C. intestinalis. By searching the C. intestinalis EST database from Ghost database which provides DNA sequences derived from actually expressed mRNA, clone ENSCINT00000010808 for CiAPEX2 and clone Ciad011a14 for CiP0 were detected as candidate homologues. For clone EN […]

library_books

NK4 Antagonizes Tbx1/10 to Promote Cardiac versus Pharyngeal Muscle Fate in the Ascidian Second Heart Field

2013
PLoS Biol
PMCID: 3849182
PMID: 24311985
DOI: 10.1371/journal.pbio.1001725

[…] ndidate 21-mer target sites were trimmed to 20 mer, and those that begin with A or G and end with A were further considered. Candidate 20 mer were BLASTed against the Ciona intestinalis genome on the Ghost database and selected to avoid polymorphic region as well as 20 mer with potential off-targets (i.e., >16 nucleotide between positions 2 and 17 on the antisense). Target sense sequences were rev […]

call_split

Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

2007
BMC Evol Biol
PMCID: 1999503
PMID: 17708769
DOI: 10.1186/1471-2148-7-143
call_split See protocol

[…] , and Ensembl and DOE Joint Genome Institute [JGI] Ciona intestinalis v2.0 [JGI site for the complete C. intestinalis genome sequence and gene annotations]: []) and a cDNA/EST database (Ref.: [], and Ghost Database: []) using human and HR IRK channel protein AA sequences [,]. IRK channel proteins were identified by using the following basic method. Briefly, when the corresponding cDNA sequence cov […]

library_books

Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage

2006
BMC Evol Biol
PMCID: 1578592
PMID: 16893461
DOI: 10.1186/1471-2148-6-60

[…] 5). The C-terminal portion of the predicted protein is confirmed by an EST [GenBank EST:BW395090.1] that includes the FReD, as well as by the 9 ESTs in Gene Cluster 02393 of the cDNA resources of the Ghost Database []. In addition, a highly-related gene product is encoded on C. savigyni contig 41574 [GenBank CoreNucleotide:AACT01041574]. The corrected C. intestinalis protein sequence has 2355 aa ( […]


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Ghost Database institution(s)
Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan; CREST, Japan Science Technology Agency, Kawaguchi, Japan
Ghost Database funding source(s)
Supported by Grants-in-Aid from MEXT, Japan (17071020), and CREST.

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