Zebra Finch assembly and gene annotation


This is the first release of the high-coverage ~6X assembly of the Zebra finch (Taeniopygia guttata) genome. The sequencing and assembly of the genome was done by the Washington University Genome Sequencing Center.

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. In the initial assembly, prior to the inclusion of 35 finished BAC clones in the final assembly, the 92,299 major contigs had an N50 length of 39kb and the 37,252 major supercontigs an N50 length of 10.4Mb.

Zebra finch has a genome of 1.2Gb in length, of which 1Gb of sequence has been ordered and orientated on the chromosomes and one linkage group, with a further 36Mb being localised to specific chromosomes or linkage groups.

Gene annotation

For the taeGut3.2.4 assembly, the predicted gene set contains 18,447 gene models, of which 17,475 are protein coding genes. The gene set was built using a modified version of the standard EnsEMBL genebuild pipeline. Unusually, some genes relying on EST evidence were included in the gene set. The evidence used to construct the gene set included alignments of EnsEMBL chicken proteins, alignments of other avian proteins and mammal protein alignments, in addition to zebra finch evidence.

In Ensembl release 67, the zebra finch gene set was updated by including the zebra finch mitochondrial (MT) annotation. The sequence and annotation for MT was added using the NCBI record DQ422742.1.

More information

General information about this species can be found in Wikipedia.



AssemblytaeGut3.2.4, Aug 2008
Database version80.1
Base Pairs1,222,864,721
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 startedAug 2008
Genebuild releasedFeb 2009
Genebuild last updated/patchedMay 2012

Gene counts

Coding genes

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

Non coding genes724
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.

Misc non coding genes15

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.19,334


Genscan gene predictions59,816
Short Variants1,666,993