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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAGgtagccttgcaatttgattatacccttatggattcacatggattgaaacatacgattacttattcgcttaatcattgttccttctacag

Basic information

species Arabidopsis thaliana
transcript AT1G20260.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20260.1 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 5'ss of exon 12
ATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAGgtag---ccttgcaatttgattatacccttatggattcacatggattgaaacatacgattacttattcgcttaat-cattgttc---cttctacag---------------------------------------
||||||||||| ||||| || ||||||||||| ||||| || |||||||||      ||||| |     |   ||||||      ||||| ||    |  |     || || ||| |     | ||| |||    |||  |  |                                       
ATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAGgtaagacttttgcagtggagctgccccctta------cacataga---gagtacctagttgctgattggaaaggtgcatggttttaactttcaaggagttaaaagtaatctttattattggtgatggatttgcag
















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|125076572|gb|EL139677.1|EL139677
EST:     ATCACTTTCTCGGCTGATGAAG                         AGTGCTATTGGTGAAGGAATGACTCG
genomic: ATCACTTTCTCGGCTGATGAAGgtagccttgc ... ccttctacagAGTGCTATTGGTGAAGGAATGACTCG
EST: gi|116471554|gb|EG514146.1|EG514146
EST:     ATGTACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGGAG                         AGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
genomic: ATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAGgtagccttgc ... ccttctacagAGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
EST: gi|125084301|gb|EL144555.1|EL144555
EST:     CTCGGCTGATGAAG                         AGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
genomic: CTCGGCTGATGAAGgtagccttgc ... ccttctacagAGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
EST: gi|86084595|gb|DR380354.1|DR380354
EST:     TCTCGGCTGATGAAG                         AGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
genomic: TCTCGGCTGATGAAGgtagccttgc ... ccttctacagAGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
EST: gi|116428286|gb|EG470878.1|EG470878
EST:     GATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG                         AGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
genomic: GATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAGgtagccttgc ... ccttctacagAGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
EST: gi|116428287|gb|EG470879.1|EG470879
EST:     AGATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAG                         AGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC
genomic: AGATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAGgtagccttgc ... ccttctacagAGTGCTATTGGTGAAGGAATGACTCGCAAAGACCATTCTGATGTGTCCAAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATACCCACCCATTAACGTGCTTCCATCACTTTCTCGGCTGATGAAGgtagccttgcaatttgattatacccttatggattcacatggattgaaacatacgattacttattcgcttaatcattgttccttctacag

- - - - - - - - - - - - - - - - - - - GCTGAT