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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccacatattcccccttcccccgcgctccatttaccggaccccgatccgatccggcatgatctcacggcggattctctggtgattggtttgtgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG

Basic information

species Zea mays
transcript GRMZM2G348866_T02
intron # 1
splice site 3'
intron type U2

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|148969459|gb|EE020269.2|EE020269
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|76021487|gb|DT948657.1|DT948657
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|76932642|gb|DV173100.1|DV173100
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211497316|gb|FL084186.1|FL084186
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|76915823|gb|DV166138.1|DV166138
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|71434350|gb|DR815400.1|DR815400
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|50334180|gb|CO529306.1|CO529306
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|86468761|gb|DY235131.1|DY235131
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGGGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211500195|gb|FL084194.1|FL084194
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|101402261|gb|EB822718.1|EB822718
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|78073578|gb|DV502012.1|DV502012
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211497318|gb|FL084188.1|FL084188
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATC-RCCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|76286853|gb|DV026421.1|DV026421
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|78119406|gb|DV537790.1|DV537790
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAGGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211497310|gb|FL084180.1|FL084180
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211497317|gb|FL084187.1|FL084187
EST:     CCGCCGCGCACGTTACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211497311|gb|FL084181.1|FL084181
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211500193|gb|FL084192.1|FL084192
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAKGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|148954829|gb|EC900302.2|EC900302
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|211497313|gb|FL084183.1|FL084183
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|71444517|gb|DR825567.1|DR825567
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|93013298|gb|EB638818.1|EB638818
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|101396950|gb|EB820400.1|EB820400
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|78111855|gb|DV530252.1|DV530252
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|71447775|gb|DR828825.1|DR828825
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|71449627|gb|DR830677.1|DR830677
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
EST: gi|71447776|gb|DR828826.1|DR828826
EST:     CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGG                         AGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
genomic: CCGCCGCGCACGTCACACTCTACGATTTCAACATCGACCTCAACCAGTGGgtgagccaca ... tgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatccggcatgatctcacggcggattctctggtgattggtttgtgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG
             atctcac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccacatattcccccttcccccgcgctccatttaccggaccccgatccgatccggcatgatctcacggcggattctctggtgattggtttgtgctgcgcagAGCCGGAAGGACGTCGAGGGGTCGCTGTTTGTCGTCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT