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. 2001 May 1;98(10):5693–5698. doi: 10.1073/pnas.101049998

Figure 2.

Figure 2

(A) Sequence identities at the 5′ ends of cDNA clones from Hydra genes. Identical 5′ sequences are in lowercase; divergent downstream sequences are in uppercase. The translation start ATG codon is separated from the 5′ untranslated region sequence by a slash. The upper group of sequences contains the spliced leader A (SL-A) sequence; the lower group contains the spliced leader B (SL-B) sequence. GenBank accession nos. for the sequences are as follows: Hint, M64611; Syk, AF060949; HTK32, AF123442; HTK54, U24116; HFZ, AF209200; Csk, AF067775; Cnash, U36275; Alx, AF295531; Pax-A, U96193; enolase, U85827; PLC-βHI, AB017511; hyGK, AF031931; ECE, AF162671; hym-323, AB40074; HTK16, U00936; HZO-1, AF230482; PKC1B, Y12857; ras1, X78597; nucleoporin, U85827; annexin XII, M83736. All genes are from H. vulgaris except hyGK (Hydra oligactis), enolase (H. oligactis), Pax-A (Hydra littoralis), and PLC-βI (Hydra magnipapillata). The three different Hint sequences (labeled Hint 1–3) arise because of alternative splicing. Hint produces a long transcript with SL-A at the 5′ end and a shorter transcript that can contain either SL-A or -B (45). The single nucleotide difference (T>G) in the SL-A sequence of HTK54 may be because of an error during cDNA synthesis or the presence of multiple alleles of SL-A. A complete copy of the SL-B sequence is located internally in a H. vulgaris cDNA for cAMP-response element-binding protein (CREB) (46), where it results in the truncation of a highly conserved portion of the CREB coding sequence. We have attempted, without success, to confirm this arrangement by amplification of the corresponding region from first-strand cDNA made from H. vulgaris polyA+ RNA. We therefore believe that this clone is a hybrid produced during cDNA library construction by ligation of the 3′ end of a partial CREB cDNA to the 5′ end of a cDNA derived from an SL-B-containing mRNA. (B) Alignment of sequences from the 5′ ends of HTK32 cDNA clones containing SL-A or -B sequences. The clone containing SL-B includes four nucleotides that are not present in the SL-A-containing message. The splice acceptor dinucleotide is underlined. The SL-A-containing sequence is from a clone isolated from a cDNA library. The SL-B-containing sequence was obtained by 5′ RACE (see Materials and Methods). (C) Genomic sequence from the Hydra Syk gene (24). The splice acceptor dinucleotide is indicated by double underlining. The genomic sequence is aligned with the sequences from Syk cDNAs containing either SL-A or -B (see A). The pyrimidine-rich sequence upstream of the splice acceptor dinucleotide is shaded.