Flycatcher assembly and gene annotation

Assembly

The FicAlb_1.4 assembly was provided by Uppsala University in January 2012. The assembly comprises 21765 toplevel sequences, all of which are unplaced scaffolds (from 30359 contigs). The N50 of the contigs is 450 kb and the N50 of the scaffolds is 7.3 Mb. 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_000247815.1

Gene annotation

FicAlb_1.4 was annotated using a standard Ensembl gene annotation system, incorporating RNAseq data provided by Uppsala University. The annotation process is described in the document below.

RNAseq data set

In addition to the Ensembl gene set, we produced RNAseq-based gene models and an indexed BAM file for each of the nine tissue sample used by the RNAseq pipeline and also for the merged data from all tissues. Each RNAseq-based gene model represents only the best supported transcript model. We did a BLASTp of these transcript models against UniProt proteins of protein existence level 1 and 2 in order to annotate the open reading frame. The best BLAST hit is displayed as a transcript supporting evidence.

A total of 12238 gene models in the Ensembl gene set include RNAseq data as supporting evidence. Of these 12238 gene models, 6793 are annotated exclusively from RNAseq data with a further 5445 gene models annotated using a combination of RNAseq data and other protein evidence. The RNAseq data were used to add UTR to protein coding models.

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

TissueNumber of gene models
brain16758
embryo17711
kidney16432
liver14916
lung15946
merged22302
muscle14963
ovary19306
skin17358
testis18812

Additional splice junctions (introns) may have been identified by our pipeline and not included in the best supported transcript model. We therefore provide users with the full set of introns identified by our RNAseq pipeline to enable further analysis. These introns were identified by searching for reads that splice when mapped to the genome.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyFicAlb_1.4, INSDC Assembly GCA_000247815.1, Jan 2012
Database version76.1
Base Pairs1,102,357,628
Golden Path Length1,116,409,277
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedMay 2012
Genebuild releasedSep 2013
Genebuild last updated/patchedSep 2013

Gene counts

Coding genes

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

15,303
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.

897
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.

66
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.16,946

Other

Genscan gene predictions37,743