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Spotted gar assembly and gene annotation


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.

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:

TissueNumber of gene models

More information

General information about this species can be found in Wikipedia.



AssemblyLepOcu1, INSDC Assembly GCA_000242695.1, Dec 2011
Base Pairs945,878,036
Golden Path Length945,878,036
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2012
Genebuild releasedDec 2013
Genebuild last updated/patchedOct 2016
Database version104.1

Gene counts

Coding genes18,341
Non coding genes4,932
Small non coding genes2,593
Long non coding genes2,313
Misc non coding genes26
Gene transcripts27,887


Genscan gene predictions30,348

About this species