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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG

Basic information

species Glycine max
transcript GLYMA02G07910.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 8
gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG
                                                                                | | |||  ||      ||  |    | |  |    | ||  || || ||   |   | | ||  | |  |||| ||  |||| || |||||||| |||||||| || || || || ||||| ||| |||| || || ||||||||| | ||||||||||||||||| || |
-------------------------------------------------------------------------------gtatgtttcatgcctctgttcctttccaatagacatgacttcattcttcttaccacgttta-attctttatagGTAACTGTTGTCAAGAATGAAGAAGGTGGAAACTCAGTGGCTACGGTTGTCTTAAGAGGCAGCACCGATAGTATATTGGATGATCTTGAAAGAGCTGTTG

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 8
gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG
                                                                 |  | ||  ||     |||| || | ||        ||| | ||  || |    ||   |   ||    |  |  | |  |||  |||| |   |  | || || ||||| ||||||||||| || || |||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |
-----------------------------------------------------------------gtatgttttctactccctttgtgcttttacagaagataactttt-tattcttccttaccaacattcattttgttttttattatatagGTTATTGTCATCAAGAACGAAGAAGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 8
gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG
                                                                 |    |||      || ||   |  | | | |||||||  | |     ||||  ||| | |||||||  ||           |  |||| ||  | || || || ||||| ||||||||||| || || ||||||||  |  |||| |||||||| |||||||||||||||||||||||||| || |
-----------------------------------------------------------------gtacgttctacctgtttttacagaagatat-atttttatttttccttggcaacattcattttttttgttta-----------tatagGTTACTGTCGTCAAGAACGAAGATGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTG

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 8
gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG
                                | || |     ||||     | | | |   |     ||     ||| ||| | || || ||  | ||  | |  ||   |||||  | | ||  | ||   |||||       |||  |||| |||||||||||||||||||| |||||||| || |||  |||||| ||||||||||||||||||||||||||| ||||||| |||||||||||||| |
------------------------------gtacttccaaacgtccac---ccctatcttcctggatatagcattttggttcatatttttcttccctttcattaccat--gatgcatgtgttttcctcttcaaataatatc----tat-tagGTCACCATTGTGAAAAATGAAGAAGGTGGAAACTCCGTATGCACTGTGGTTTTACGAGGAAGTACTGATAGTATATTAGATGACCTTGAAAGAGCAGTTG

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|151397877|gb|EV267750.1|EV267750
EST:     ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
genomic: ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
EST: gi|193420636|gb|FK390559.1|FK390559
EST:     ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGT
genomic: ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTG-AAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGT
EST: gi|193347893|gb|FK312785.1|FK312785
EST:     ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
genomic: ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
EST: gi|14011960|gb|BG726882.1|BG726882
EST:     ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
genomic: ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
EST: gi|193427201|gb|FK393451.1|FK393451
EST:     ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
genomic: ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
EST: gi|298187661|gb|HO034810.1|HO034810
EST:     TCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
genomic: TCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
EST: gi|254342218|gb|GR853355.1|GR853355
EST:     ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGG                         GTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT
genomic: ATCTTGGATATGTAGATTCCGTTTCAGTTCAGGAAATTGGTGGTGTCAGGgtatgttaaa ... tgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG
                  aattttcttatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaaagctggattctttcagttctgtcattttctgggttccatgtttcttttttattttagcttattcccttgcttctttttgttgttgtcatttttaagtattgcatgcaattttcttattttttggataatgatatgatatgcagGTGACCATTGTGAAAAATGAAGAGGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG