Lamprey assembly and gene annotation

Assembly

Petromyzon_marinus_7.0 is an assembly of the sea lamprey (Petromyzon marinus) provided by the lamprey consortium. It was sequenced to a total of 5.0X whole genome coverage. The combined WGS and BAC-end sequence reads were assembled using Arachne V3.2. The expected genome size is 1.92 gb. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of scaffolds is 184.619 kb. The total of all scaffolds is 885Mb

Gene annotation

The gene set for lamprey was built using the Ensembl pipeline. Gene models are based on genewise alignments of lamprey proteins and most proteins from Uniprot, whether vertebrate or more genetically distant species. The protein based gene models were then extended using lamprey cDNA. To improve the accuracy of models generated from distant species, transcriptome data was used to filter out the different gene models. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyPmarinus_7.0, Jan 2011
Database version76.7
Base Pairs647,368,134
Golden Path Length885,550,958
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedFeb 2011
Genebuild releasedSep 2011
Genebuild last updated/patchedApr 2013

Gene counts

Coding genes

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

10,415
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, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, 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.

2,652
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.

47
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.14,141

Other

Genscan gene predictions34,895