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.

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

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
Database version77.1
Base Pairs1,102,357,628
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 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).

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.


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.16,946


Genscan gene predictions37,743