Spotted gar assembly and gene annotation

Assembly

This site displays annotation on version 1 (January 2012) of the spotted gar (Lepisosteus oculatus) genome assembly, known as 'LepOcu1'.

It was produced by the Broad Institute of MIT and Harvard. The primary assembly comprises 29 chromosomes and 1,896 unplaced scaffolds. The collection of 45,199 contigs included in this assembly have an N50 value of 68kb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

Gene annotation

The spotted gar LepOcu1 assembly was annotated using the standard Ensembl gene annotation system incorporating RNASeq data. The annotation process is described in the document below.

• Detailed information on genebuild (PDF)

RNASeq data set

In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt vertebrate proteins of protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence.

The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:

More information

General information about this species can be found in Wikipedia.