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.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000242695.1

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
Brain17523
Embryo18376
Eye18017
Heart16323
Kidney18037
Larvae18577
Liver16487
Muscle14740
Skin17959
Testis18409
Merged19683

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyLepOcu1, INSDC Assembly GCA_000242695.1, Dec 2011
Database version78.1
Base Pairs869,417,849
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).

945,878,036
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJan 2012
Genebuild releasedDec 2013
Genebuild last updated/patchedDec 2013

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

18,341
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.

2,619
Pseudogenes

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.

42
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

Other

Genscan gene predictions30,348