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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccacttctcttatttcatcttttacaaatctggtctttggttttcctgcacatacctcctctatgttactctctcacttgtgcgcctattgcttttttactatgcgatctctcttatgaaacagATTGGTTATTTGGATATATGGGAAGCAGCTACATTGTCTATTAAGAAAGAAGGCTACAGCATCAAACCTACTAATGACCCTGTAATTACAGAAAAGTTCT

Basic information

species Arabidopsis thaliana
transcript AT5G08440.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 17
gtatg-ccacttctcttatttcatct--tttacaaatctg-gtc--tttggttttcctgcacatacctcctctatgttactctctcacttgtgcgcctattgcttttttactatgc--gatctctcttatgaaacagATTGGTTATTTGGATATATGGGAAGCAGCTACATTGTCTATTAAGAAAGAAGGCTACAGCATCAAACCTACT------AATGACCCTGTAATTACAGAAAAGTTCT
||||| | | | |    | | |  ||  |||| || |||  ||   | | ||||| ||    |   ||  ||      |     |   ||     |   ||  |      ||  ||  ||    | | ||    |||  ||| ||| | |||||||||||| ||||||| ||| | |||||||  ||||| |||||||||||   ||||      | ||   ||||| |  | || |      
gtatgactattacaacaaatacccctagtttataattctttgttgatcttgttttgctatcaaagtcttatcaggaacatatgtttttttaatttcaccttcttaaagagcttagcctgaatcttttaattttgcagGCTGGATATCTTGATATATGGGAACCAGCTACTTTGGCCATTAAGAGGGAAGGTTACAGCATCAAGTGTACTGGACCTAGTGGTGCTGTAGTCTCTGAGA------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|164042461|gb|ES187363.1|ES187363
EST:     TAGAGAAGAGTCTTTATAACGGTCATGCTTTATTCAAAGTCTCCTATTCA                         ATTGGTTATTTGGA
genomic: TAGAGAAGAGTCTTTATAACGGTCATGCTTTATTCAAAGTCTCCTATTCAgtatgccact ... tatgaaacagATTGGTTATTTGGA
EST: gi|116441739|gb|EG484331.1|EG484331
EST:     TAGAGAAGAGTCTTTATAACGGTCATGCTTTATTCAAAGTCTCCTATTCA                         ATTGGTTATTTGGATATATGGGAAGCAGCTACATTGTTTATTAAGAAAGAA
genomic: TAGAGAAGAGTCTTTATAACGGTCATGCTTTATTCAAAGTCTCCTATTCAgtatgccact ... tatgaaacagATTGGTTATTTGGATATATGGGAAGCAGCTACATTGTCTATTAAGAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcacttgtgcgcctattgcttttttactatgcgatctctcttatgaaacagATTGGTTATTTGGATATATGGGAAGCAGCTACATTGTCTATTAAGAAAGAAGGCTACAGCATCAAACCTACTAATGACCCTGTAATTACAGAAAAGTTCT
 ctctcac  putative branch site (score: 3)
                                      tctctcttat  putative PPT
                       ttttttactat  TA-rich tract