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.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000242695.1
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:
|Tissue||Number of gene models|
General information about this species can be found in Wikipedia.
|Assembly||LepOcu1, INSDC Assembly GCA_000242695.1, Dec 2011|
|Golden Path Length|
The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).
|Genebuild method||Full genebuild|
|Genebuild started||Jan 2012|
|Genebuild released||Dec 2013|
|Genebuild last updated/patched||Dec 2013|
Genes and/or transcript that contains an open reading frame (ORF).
|Non coding genes||2,619|
|Small non coding genes|
Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.
|Misc non coding genes||26|
A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.
|Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.||25,144|
|Genscan gene predictions||30,348|