Examples of dog cDNAs that have incorporated a SINEC_Cf (–) sequence via a splice acceptor site within the element
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SINEC_Cf(–) |
TTTTTATTTATTTATGATAGTCACACAGAG.. 141.. GGATCCC |
|---|---|---|
| 1 | BM540124(+) | 38-GCCCCGGAGG TCACACACAC.. 134.. GGATCCC AGGTCATCAC-208 |
| Cfa30 | 33601222-GCCCCGGAGGgtgagagctg... tttatgatagTCACACACAC.. 136.. GGATCCC AGGTCATCAC-33600139 | |
| 2 | CN002508(+) | 154-CACTGATGAG TCACACAGAG.. 138.. GGATCCC CATTTCATTT-328 |
| Cfa2 | 68067110-CACTGATGAGgtatgaattg... tttatgatagTCACACAGAG.. 138.. GGATCCC CATTTCATTT-68064412 | |
| 3 | CO675838(–) | 306-GCACACTCTG TCACACAGAG.. 138.. GGATCCC AAGCCAAGCA-478 |
| Cfa6 | 11279927-GCACACTCTGgtcagttcca... tttatgatagTCACACAGAG.. 141.. GGATCCC AAGCCAAGCA-11279642 | |
| 4 | BM536886(+) | 177-CAGCCCACAG ACATAGAGAG.. 134.. GGATCCC CTCATCTGAC-347 |
| Cfa9 | 26197334-CAGCCCACAGgtaaagtatt... ttcatgatagACATAGAGAG.. 134.. GGATCCC CTCATCTGAC-26192495 | |
| 5 | CO668671(–) | 109-CATCCCAGAG GCNCNCAGTG.. 136.. GGATCCC CTACATTGCT-281 |
| Cfa14 | 47081174-CATCCCAGAGgtaagagtat... tttatgatagGCACACAGTG.. 138.. GGATCCC CTACATTGCT-47047028 | |
| 6 | BU749657(+) | 322-GCAATCACGG AGAGAGAGAG.. 114.. GGATCCC CGGGTTAAGG-472 |
| Cfa15 | 52463523-GCAATCACGGgtaaggtctt... tttattatagGCACACAGTG.. 114.. GGATCCC CGGGTTAAGG-52469700 | |
| 7 | BQ234114(+) | 233-CCCACCACAG TCACAGAGAG.. 136.. GGATCCC AGATCCATCT-405 |
| Cfa26 | 24551559-CCCACCACAGgtataaacaa... tcagtcacagTCACAGAGAG.. 136.. GGATCCC AGATCCATCT-24550169 | |
| 8 | CO684930(–) | 328-ATCAAAGCTG TCACACAGAG.. 132.. GGATCCC CATGTGTGTG-496 |
| Cfa27 | 34794751-ATCAAAGCTGgtgagataca... tctatgatagTCACACAGAG.. 138.. GGATCCC CATGTGTGTG-34795736 | |
| 9 | CO675560(–) | 183-TCTTCAAGCT TCACAGAGAG.. 134.. GGATCCC CCGTTAGTTG-353 |
| Cfa22 | 49073614-TCTTCAAGCTgtgagtgcgg... TTAGTTG-49088654 | |
| 10 | CO629118(–) | 320-ACCTCTAAAG TCNCAGAGAG.. 134.. GGATCCC TATGCTCACT-493 |
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Cfa35
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28868224-ACCTCTAAAGgtcagtcaca... TATGCTCACT-28867050
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The location of the splice site (↓) follows a canonical “AG” dinucleotide, and is illustrated on the consensus SINEC_Cf (–) sequence. For examples 1–8, the GenBank accession numbers (and orientations) refer to dog ESTs [e.g., BM540124 (+)] that can be aligned with specific chromosomal regions of the dog genome sequence. The alignments of EST and genomic sequences include exons (upper case), introns (lower case), and coordinates of the aligned EST and genomic sequences. All introns are flanked by canonical “gt” and “ag” dinucleotides. For examples 9 and 10, sequences that flank the SINEC_Cf of the EST can be aligned with genomic sequence, but the SINEC_Cf sequence is absent. These are examples of bimorphic SINEC_Cf insertions that have become incorporated within cDNAs as alternative exons. For three of the dog ESTs (CN002508, BM536886, CO668671), the SINE insertion disrupts the open reading frame of the homologous human cDNA (phosphorylase kinase, β subunit, NM_000293; TRIM37 mRNA, NM_015294; phosphodiesterase 1C mRNA, NM_005020).
