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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttgttttttatatttgataatctgttgtggtttcagaaataggttggaaagtatggaacagagtgagcctagcagacatgaacttcaaaaattctcccttggctattgcttttctgtctattttcgggccatcagttgaagttgatatacctctttgtttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG

Basic information

species Glycine max
transcript GLYMA02G40310.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtatttgttttttatatttgataatctgttgtggtttcagaaataggttggaaagtatggaacagagtgagcctagcagacatgaacttcaaaaattctcccttggctattgcttttctgtctattttcgggccatcagttgaagttgatatacctctttgtttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG
                                                                    |  | ||      | |  |   || | |  ||   | | ||| | || ||| |  | ||||      | |||   |     ||   ||  || |||| | | | ||||||| || || || |||||||||||||| |||||||| || || ||| |||||||||||||||||||||||||| | || ||| ||
-------------------------------------------------------------------tgcctaagatcca-aaatttttgctgccatgatggacacatggatgtttcttgta-gcctat------gacattcttaactcttttgatggctatttggtgtgtccagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG

upper sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S386_20V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaagtatttgttttttatatttgataatctgttgtggtttcagaaataggttggaaagtatggaacagagtgagcctagcagacatgaacttca--aaaattctcccttggctattgcttttctgtctattttcgggccatc----agttgaagttgatatacctc---tttgtttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG
                                                                                    | || ||| |   |  ||  |    ||  || || |||   |   |  |        ||    | |  ||   ||| |   |    |    || || |||||||||||||||| |||  ||| |||||||||||||| ||||| ||||| |||||||||||  | |||||||| || |||||| ||
------------------------------------------------------------------------------------cctgcactccttcagcatgttgttctgcataatgttttctggaagaagtcgaaagtttcgcaaattctaataggatgtgttttggatcctcttgttgcagATGAATACGTTATGTGCAATGGTTGCAAGAGTCCGGACACTATCCTTACGAAGGAGAATCGGTTGTTCTTTCTTCGTTGTGAGCAG
















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|209719242|gb|BW679797.1|BW679797
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|12691100|gb|BG157436.1|BG157436
EST:     GCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|207760750|gb|GD734073.1|GD734073
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|192332834|gb|FK026835.1|FK026835
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTTTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|21479883|gb|BQ576566.1|BQ576566
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTNATC-GTCTTGGGTGCAAGAGTCCGGATACTATACTTACA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTT-ATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACA
EST: gi|151412916|gb|EV282728.1|EV282728
EST:     GGAAAGTTTGCACCAAAGAACTTTGAAAGGA-TTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCCGGATACTATACTTACA
genomic: GGAAGGTTTGCACCAAAGAACTTTGAA-GGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCC-GGATACTATACTTACA
EST: gi|209728549|gb|BW663549.1|BW663549
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|192323866|gb|FK018617.1|FK018617
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|209725552|gb|BW677854.1|BW677854
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|254337821|gb|GR849560.1|GR849560
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|213611450|gb|DB976885.1|DB976885
EST:     GGAAGGTTTGCACCAAAGAACTTTGAAGGAAT-CAAGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCT-GCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|58022083|gb|CX708824.1|CX708824
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|8827357|gb|BE211087.1|BE211087
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|214007895|gb|DB986470.1|DB986470
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|58020605|gb|CX707347.1|CX707347
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|254337820|gb|GR849559.1|GR849559
EST:     GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAA
EST: gi|16347705|gb|BI973300.1|BI973300
EST:     GGGAAGGTTTGCACCACAGAACTTTGAAGGAATTCTGCGACGATATGTCA                         ATGAATACGTCATTTGCCTT
genomic: GGGAAGGTTTGCACCAAAGAACTTTGAAGGAATTCTGCGACGATATGTCAgtaagtattt ... tttttttcagATGAATACGTTATTTGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtctattttcgggccatcagttgaagttgatatacctctttgtttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG
                           agttgat  putative branch site (score: 5)
                                   tacctctttgtttttt  CT-rich tract
                                         tttgttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttgttttttatatttgataatctgttgtggtttcagaaataggttggaaagtatggaacagagtgagcctagcagacatgaacttcaaaaattctcccttggctattgcttttctgtctattttcgggccatcagttgaagttgatatacctctttgtttttttcagATGAATACGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTACAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA