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Flycatcher assembly and gene annotation


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.

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

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.



AssemblyFicAlb_1.4, INSDC Assembly GCA_000247815.1, Jan 2012
Base Pairs1,102,357,628
Golden Path Length1,116,409,277
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2012
Genebuild releasedSep 2013
Genebuild last updated/patchedJul 2016
Database version100.1

Gene counts

Coding genes15,303
Non coding genes6,539
Small non coding genes785
Long non coding genes5,642
Misc non coding genes112
Gene transcripts23,376


Genscan gene predictions37,743

About this species