Table 2

Comparison of ASU, NCBI and Ensembl gene annotations of the A. carolinensis genome
Overview ASU NCBI Ensembl
Annotated genes 22,962 15,645 17,792
Annotated transcript isoforms 59,373 16,533 18,939
Annotated isoforms/gene 2.59 1.06 1.06
Annotated Transcripts
All transcript isoforms 59,373 16,533 18,939
Transcripts with start & stop codons 53,401 14,667 4,170
Transcripts missing start or stop codon 5,972 1,866 14,769
Single exon transcripts 2,070 983 364
Transcript N50 length 5,355 2,364 2,037
Average coding sequence length 1,964 1,701 1,531
Exons
Total number of exons 229,204 156,742 174,545
Exons with start with codon 29,677 13,512 5,971
Exons without start or stop codon 168,367 128,486 158,935
Exons with stop codon 29,727 13,779 9,278
Exons/annotated transcript 12.05 10.11 9.62
Average exon length 170 170 160
Total exon length 38,902,806 26,658,387 27,910,718
3' UTR
Total transcripts with 3'UTR 34,926 5,861 0
Average length of transcripts with 3'UTR 1,168 456 0
Total 3'UTR sequence length 40,798,794 2,674,388 0
5' UTR
Total transcripts with 5'UTR 46,782 6,168 0
Average length of transcripts with 5'UTR 244 86 0
Total 5'UTR sequence length 11,422,626 527,454 0
Introns
Total number of introns 192,418 141,362 155,949
Average intron length 4,525 4,463 2,553
Total intron sequence length 870,771,088 630,937,171 398,124,572

Eckalbar et al.

Eckalbar et al. BMC Genomics 2013 14:49   doi:10.1186/1471-2164-14-49

Open Data