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Title: Last Annotation of Fugu rubripes at JGI


No abstract prepared.

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Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director. Office of Science. Office of Biological andEnvironmental Research, Lawrence Livermore National Laboratory, LosAlamos National Laboratory
OSTI Identifier:
Report Number(s):
R&D Project: 626739; BnR: KP1103010; TRN: US200602%%27
DOE Contract Number:
Resource Type:
Resource Relation:
Conference: Hinxton Fish Workshop, Cambridge, UK,11/24-25/2005
Country of Publication:
United States

Citation Formats

Salamov, Asaf, Terry, Astrid, Putnam, Nicholas, Rokhsar, Dan, Grigoriev, Igor, Loh Eddie, and Venkatesh, Burappa. Last Annotation of Fugu rubripes at JGI. United States: N. p., 2005. Web.
Salamov, Asaf, Terry, Astrid, Putnam, Nicholas, Rokhsar, Dan, Grigoriev, Igor, Loh Eddie, & Venkatesh, Burappa. Last Annotation of Fugu rubripes at JGI. United States.
Salamov, Asaf, Terry, Astrid, Putnam, Nicholas, Rokhsar, Dan, Grigoriev, Igor, Loh Eddie, and Venkatesh, Burappa. Tue . "Last Annotation of Fugu rubripes at JGI". United States. doi:.
title = {Last Annotation of Fugu rubripes at JGI},
author = {Salamov, Asaf and Terry, Astrid and Putnam, Nicholas and Rokhsar, Dan and Grigoriev, Igor and Loh Eddie and Venkatesh, Burappa},
abstractNote = {No abstract prepared.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Nov 22 00:00:00 EST 2005},
month = {Tue Nov 22 00:00:00 EST 2005}

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  • Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward thismore » aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.« less
  • The p55 gene, which codes for a 55-kDa erythrocyte membrane protein, has been cloned and sequenced from the genome of the Japanese puffer fish Fugu rubripes (Fugu). This organism has the smallest recorded vertebrate genome and therefore provides an efficient way to sequence genes at the genomic level. The gene encoding p55 covers 5.5 kb from the beginning to the end of the coding sequence, four to six times smaller than the estimated size of the human gene, and is encoded by 12 exons. The structure of this gene has not been previously elucidated, but from this and other datamore » we would predict a similar or identical structure in mammals. The predicted amino acid sequence of this gene in Fugu, coding for a polypeptide of 467 amino acids, is very similar to that of the human gene with the exception of the first two exons, which differ considerably. The predicted Fugu protein has a molecular weight (52.6 kDa compared with 52.3 kDa) and an isoelectric point very similar to those of human p55. In human, the p55 gene lies in the gene-dense Xq28 region, just 30 kb 3{prime} to the Factor VIII gene, and is estimated to cover 20-30 kb. Its 5{prime} end is associated with a CpG island, although there is no evidence that this is the case in Fugu. The small size of genes in Fugu and the high coding homology that they share with their mammalian equivalents, both in structure and sequence, make this compact vertebrate genome an ideal model for genomic studies. 23 refs., 3 figs.« less