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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCACTGGAATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttgcttcctgtttagtacttgttggtctcattccttgtcattaatcacgacatgcatatcatatccacactgcag

Basic information

species Glycine max
transcript GLYMA15G01980.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01980.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 5'ss of exon 16
GCATCACTGGAATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttgcttcctgtttagtacttgttggtctcattccttgtcattaatcacgacatgcatatcatatccacactgcag
|| ||| | |||||||||||  ||||||| || || |||||||| |||||||| |||||||| |||  || |         | | || ||    |||        |||   |  | |  |  |    || |   || |||||
GCCTCATTAGAATCTATTCGGAATTCTCTGGCAGAGGAGTTGGTGAAAATGACTGAACAGgtaaatcctgatgaaccaacggaagtttttttattcaactaccaacatgtgt-gcaaactaaactaaattttttcaatgcag

upper sequence: GLYMA15G01980.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 5'ss of exon 16
GCATCACTGGAATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttgcttcctgtttagtacttgttggtctcattccttgtcattaatcacgacatgcatatcatatccacactgcag
|||||  ||||| | || || || ||||||||||| ||||| ||  |||||||||| |||||||||||| | ||   |||   | |  ||  |  |||  | | | |||  | |      | ||    |       || |||
GCATCCATGGAAGCCATCCGTGACTCTCTTGCTGAGGAGTTAGTTCAAATGACAGAGCAGgtgaatttt-catctgttttcacattgatttatgacatctcatcttatt--ttagcttgagaatcctttgcattggctacag
















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|23729889|gb|BU763051.1|BU763051
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
EST: gi|151408005|gb|EV277820.1|EV277820
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
EST: gi|120530587|gb|EH258720.1|EH258720
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
EST: gi|21602173|gb|BQ612504.1|BQ612504
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGGCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
EST: gi|15813354|gb|BI785629.1|BI785629
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
EST: gi|151407143|gb|EV276958.1|EV276958
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG
EST: gi|17400350|gb|BM177132.1|BM177132
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTG
EST: gi|10843601|gb|BF067198.1|BF067198
EST:     AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAG                         TGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACCATCAGAG
genomic: AATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttg ... cacactgcagTGTGAGAAGTTGCGTGGGGAGGCTGCTGTATTACCTGGCTTACGATCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCACTGGAATCTATTCGCGATTCTCTTGCTGATGAGTTGGTCAAAATGACAGAACAGgtgaattttgcttcctgtttagtacttgttggtctcattccttgtcattaatcacgacatgcatatcatatccacactgcag

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