Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

Table 7 Identification and analysis of the catfish polyadenylation signal (PAS)

Hexamer	Number of transcripts	Found in catfish¹	Found in salmon²	Found in human³
AAUAAA	1,264	+	+	+
AUUAAA	435	+	+	+
AAAAAA	47	+
UAUAAA	25	+	+	+
AAGAAA	23		+	+
AAUATA	20	+	+	+
CAUAAA	19			+
AACAAA	18
AAUACA	18			+
AAUGAA	16			+
AGUAAA	15	+		+
AAUAAU	10
ACUAAA	10			+
AAUUAA	10

A subset of the full-length transcripts with polyA tails generated from sequencing were selected for analysis. Most common PAS alternatives (hexamers with single-base variant of AAUAAA) were identified within 35 nucleotides upstream of the polyA tail from full-length transcripts. ¹Alternative PAS identified in Chen et al. (2010) [15]; ² Alternative PAS identified in Andreassen et al. (2009) [25]; and ³Alternative PAS identified in Macdonald et al. (2002) [37].

ISSN: 1471-2164