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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT

Basic information

species Glycine max
transcript GLYMA18G17590.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttct-ttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
                                                                                        || |  |||   |   | | ||| | ||| | |  |  |  |   | || | |||   |    |||| ||      |     ||   |||||   | ||  |   ||||||| |||||||| ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   |||||
---------------------------------------------------------------------------------------ttaaaggttcaactggatcttagtct-tcagtgttcgttcagt---agctag-gttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---agGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
                                                                                             ||    |   | | ||| | ||| | |  |  |  |   | || | |||   |    |||| ||      |     ||   |||||   | ||  |   ||||||| |||||||| ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   |||||
-------------------------------------------------------------------------------------------ggttcaactggatcttagtct-tcagtgttcgttcagt---agctag-gttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---aggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G106574_T01 (Zea mays), 3'ss of exon 2
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
                                                                                        |     |    |   | | ||| | ||| | |     | ||   | || | |||   |    |||| |       ||    ||   |||||   | ||| |   ||||||| ||||| || ||||| || |||||||| |||||||| ||||||||||||||||| || || ||||||||||||   |||||
--------------------------------------------------------------------------------------actttggctcaactggatcttagtct-tcactgttcattcaat---agctag-gtttgctgacattttgaggacaatatttctaacacaatttaccattttaa---agGCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT

upper sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattc--acttgttctgttacgaaaacttcaggc---tgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
              |  || |  |   || ||||| ||  || | | |||   |||  |  | |  | |||   ||  |   | |   |  | ||    |   | |  | |  |         || |      ||| ||    || |  ||| |      | | ||   ||   |  | | ||| |   |||| || |||| ||||||||||||||||| ||||||||||| |||||||| ||||| || |||||||| || || ||||| ||||||| ||||||
------------gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgta---atctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT

upper sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaa--ttagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
                                                                                   | ||   | |||| ||| || |  ||  | |  |  ||  | |      || | |  ||||  |||   | |||   ||||| |           ||| |   | || || |||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || |||||||||||||  |||||
--------------------------------------------------------------------------------aattagg--tcgatttgtttcttataaagcatatatagatgaaatcgggaacaatttgctttaaatttaacatcttttggtttgggt-----------ttttt---tcttttgcagGCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATT

upper sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaat-ctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
                                                                                              |    ||||||| | |||   ||| || |||  | ||| ||  | | |||   | | ||  |     | |||| | |     || ||| |   ||    |||| |||||||||||||| || || || ||||| |||||||| ||||| ||||||||||||||||| |||||||| ||||| |||||
------------------------------------------------------------------------------------------tgtgtgtagtattttttatttttgaaatactttgaattgtgtcaa--gcacttatccatgtttacttgtaattgataaacattgtcatctgtaa---ttgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT

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|193729270|gb|FK665224.1|FK665224
EST:     GTGAATTACATTGCATTGGGTTCTATCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|151408566|gb|EV278374.1|EV278374
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCCCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|208250862|gb|GE046499.1|GE046499
EST:     GTGAATTACATTGCA-TGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|208163873|gb|GD963639.1|GD963639
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|208283758|gb|GE088996.1|GE088996
EST:     GAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|42722515|gb|CK768414.1|CK768414
EST:     ATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: ATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|193484116|gb|FK449772.1|FK449772
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCT
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCT
EST: gi|26046065|gb|CA783407.1|CA783407
EST:     GTGAA-TCCTTTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|31465662|gb|CD407690.1|CD407690
EST:     TGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: TGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|192326871|gb|FK015128.1|FK015128
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCGAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|19453331|gb|BM954741.1|BM954741
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|193587621|gb|FK542656.1|FK542656
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|193363862|gb|FK329668.1|FK329668
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|193329922|gb|FK294528.1|FK294528
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|13790432|gb|BG653023.1|BG653023
EST:     ATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: ATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|298166319|gb|HO009290.1|HO009290
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCACGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|208079178|gb|GD873140.1|GD873140
EST:     GCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAG
genomic: GCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|193452514|gb|FK417534.1|FK417534
EST:     GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: GTGAATTACATTGCATTGGGTTCTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|8283605|gb|BE021164.1|BE021164
EST:     AGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: AGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
EST: gi|13478641|gb|BG508037.1|BG508037
EST:     CTAGCAGCGTATTTCACTCACCATGCAG                         GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA
genomic: CTAGCAGCGTATTTCACTCACCATGCAGgtagagagaa ... ttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
 agttaat  putative branch site (score: 4)
           tttttaaatttggata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattcacttgttctgttacgaaaacttcaggctgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT