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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCGATGAAGGAGCTTAGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagattgcattgagcttatattattctcttcactcacttgatctcttcttttcttgtgacttacttatgattcctgaaacag

Basic information

species Arabidopsis thaliana
transcript AT5G51940.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G51940.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G013600_T01 (Zea mays), 5'ss of exon 5
ATTGCGATGAAGGAGCTTAGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgag-agattgcattga---gcttatattattctcttcactcacttgatctcttcttttcttgtgacttacttatgattcctgaaacag
||||||||||||||||||||   ||| |||||||| ||||| || ||||| || ||||||||||| ||||||| |  ||  | |||   ||    | |  | | |     || ||   || |  |||  |||| | ||||||    ||  | ||||||
ATTGCGATGAAGGAGCTTAGAGCGCGCAAGATACCCTTCACGATCAGACGGTACCTACCTGATGGAAGgtgagtattttctaatgaaaagccctcacttatttttatgaacaattttactatattttcattgttaattacttc--gttgat-aaacag
















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|86024724|gb|DR320477.1|DR320477
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGA
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGA
EST: gi|86075593|gb|DR371350.1|DR371350
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
EST: gi|86024719|gb|DR320472.1|DR320472
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
EST: gi|86024715|gb|DR320468.1|DR320468
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAA
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAA
EST: gi|164066921|gb|ES122962.1|ES122962
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTC
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTC
EST: gi|164194381|gb|ES056985.1|ES056985
EST:     AGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
genomic: AGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
EST: gi|86024721|gb|DR320474.1|DR320474
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAAT
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAAT
EST: gi|86024722|gb|DR320475.1|DR320475
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGG
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGG
EST: gi|86024720|gb|DR320473.1|DR320473
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCAT
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCAT
EST: gi|86024726|gb|DR320479.1|DR320479
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTTGATCGTGGAAGACTCATGGAAAA
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACT-GATCGTGGAAGACTCATGGAAA-
EST: gi|163992189|gb|ES103112.1|ES103112
EST:     ACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
genomic: ACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
EST: gi|86024729|gb|DR320482.1|DR320482
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGG
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGG
EST: gi|86024713|gb|DR320466.1|DR320466
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAAT
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAAT
EST: gi|86024728|gb|DR320481.1|DR320481
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGA-CTGATCGT
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGT
EST: gi|86024717|gb|DR320470.1|DR320470
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACG
EST: gi|86024727|gb|DR320480.1|DR320480
EST:     AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAG                         TTTCGAGGAATGGGGAGTTGAT
genomic: AGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagatt ... cctgaaacagTTTCGAGGAATGGGGAGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCGATGAAGGAGCTTAGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGgtgagagattgcattgagcttatattattctcttcactcacttgatctcttcttttcttgtgacttacttatgattcctgaaacag

- - - - - - - - - - - -  GGAAGA