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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtattattttaataaaccatggtgtttttattgtcgagctacggtttctgctttgtggtatgttccaatccttaaactagaattaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC

Basic information

species Glycine max
transcript GLYMA13G16570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 3'ss of exon 3
-------------------gctgtattattttaataaaccatggtgtttttattgtcgagctacggtttctg----ctttgtggtatgttccaatccttaaactaga---attaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
                   |         |||||  ||  |     ||||  ||||   | |  | || ||     |||| | |||||| |   | | |    | ||    || ||| |  | ||||||| || ||||| ||||| ||||||||||| || || || ||||| |||||||| |||||||| || |||||||| |||||||| ||||| || || ||
gtatctatgcttacggtaagtgaagaaggtttaaagaa--acaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 3
gctgtatt-attttaataaaccatg-gtgtttttattgtcgagctacggtttctgctttgtgg--tatgttccaat----ccttaaactagaattaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
   ||||| ||  | ||      || ||       |     |||||   ||| || ||| ||   ||  ||  ||      || |  |  |  |   || |   ||||||||||||||||| ||||| ||||||||||| || || || |||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || ||
---gtatttatgcttatggtatgtgtgtaggaacttgaaaaagctatcttttgtgatttatgtcttagattagaacattatctcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 3
gctgtattattttaataaaccatggtgtttttattgtcgagctacggtttctgctttgtggtatgttccaatccttaaactagaattaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
   ||||   | ||  ||           | | ||       |  | ||| ||  ||    ||       ||| | |  |  |  |   || |   ||||||||||||||||| ||||| ||||||||||| || || || |||||||| ||||| |||||||| ||||| |||||||||||||| |||||||| || ||
---gtatgtgtgtaggaacttgaaaaagctatctt------ttgtgatttatgtcttagattagaacattatc-tcatgcgtgcttctgttttttcttagGTTTTGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATCGTCCCCTTCTGTAAGGGTCTTGATGTGATTCAACAGGCTCAGTCTGGTACTGGGAAAACAGC

upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------gctgtattattttaataaaccatggtgtttt-tattgtcgagctacggtttctgctttgtggtatgttccaatccttaaactagaatta--attgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
                                         ||  ||| |||   |  |   | || |||| | ||||     |      |  |   |||      |    | ||| | | | |  ||   |||   | |||||||| |||||||| ||||| ||||||||||| || ||  |||| ||||||||||| |||||||| || ||||| ||||| ||||||||||| ||||| ||
gtaagtgaagtatttcctttgagaacacattctatacataccttcattgtttctgtctagttttgtattttcttttgtttgtttcaaagcttagtactgttactcttaaacaacctcatattggttttgttatttatcattagGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATTCCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGC

upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54270.1 (Arabidopsis thaliana), 3'ss of exon 3
----gctgtattattttaataaaccatggtgtttttattgtcgagctacggtttctg----ctttgtggtatgttccaatccttaaactaga---attaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
    |         |||||  ||  |     ||||  ||||   | |  | || ||     |||| | |||||| |   | | |    | ||    || ||| |  | ||||||| || ||||| ||||| ||||||||||| || || || ||||| |||||||| |||||||| || |||||||| |||||||| ||||| || || ||
gtaagtgaagaaggtttaaagaa--acaaccttttgtttgttatgttgggattcctattaactttatcgtatgtgctctttcctgtgattgattggttgatttttttctagGTTTCGAAAAGCCTTCTGCTATTCAGCAAAGAGGAATTGTACCCTTTTGCAAGGGTCTTGATGTGATCCAGCAGGCACAGTCTGGTACTGGAAAAACCGC

upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 2
gctgtattattttaataaaccatggtgtttttattgtcgagctacggtttctgctttgtg-gtatgttccaatccttaaactagaattaattgtgctt-tagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
  |||||  |  ||      | ||    |||  ||  |    |  | |||    |      ||  || |||    || ||  |    ||||| | | | |||||||||| || || ||||| ||||||||||| || || |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||
--tgtatattgatatgttttcgtgaaaatttcttttcctccgtttgttttgcattgctcatgtcagtaccatcaattgaaagatggataattcttcgtgtagGTTTTGAAAAACCTTCTGCAATTCAGCAAAGAGGAATTGTTCCCTTTTGCAAGGGACTTGATGTAATTCAGCAAGCTCAGTCAGGAACAGGAAAGACTGC

upper sequence: GLYMA13G16570.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S31_150V6.5 (Physcomitrella patens), 3'ss of exon 3
gctgtattattt-taataaaccatggtgtttttattgtcgagctacggtttctgctttgtggtatgttccaatcct-taaactagaattaattgtgcttta--gGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
  || ||  ||| |         |||||||  || | ||   |||| |        |||        ||   | || ||| ||     |  |||  || ||  |||||||||||||||||||| || || ||  | || || |||||||||  |||||| |||||||| ||||| || || |||||||||||||| ||||| ||
-ttgcatgttttgtgggtgcttgtggtgttcgtagtttc---ctaccgagaaccaattgaaccgcactctgctgctctaatctcattctggttgacctgtacagGTTTTGAGAAGCCATCTGCTATCCAACAGCGTGGAATCGTTCCCTTCACCAAGGGTCTTGATGTCATTCAACAAGCCCAGTCTGGAACTGGCAAGACAGC

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|209702283|gb|BW677978.1|BW677978
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|213611789|gb|DB958883.1|DB958883
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|18848532|gb|BM567716.1|BM567716
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|192324821|gb|FK018797.1|FK018797
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|213599313|gb|DB962322.1|DB962322
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|209702379|gb|BW656354.1|BW656354
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|10846840|gb|BF071428.1|BF071428
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|213590331|gb|DB970129.1|DB970129
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|209710996|gb|BW681346.1|BW681346
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|213600814|gb|DB968820.1|DB968820
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|16349138|gb|BI974733.1|BI974733
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|213607320|gb|DB965150.1|DB965150
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
EST: gi|7686567|gb|AW757215.1|AW757215
EST:     TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATG                         GTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA
genomic: TGACGCTATGGGTTTGCAGGAAAATCTTCTCAGGGGAATTTACGCATATGgtattttaaa ... tgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttctgctttgtggtatgttccaatccttaaactagaattaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC
                                      aattaat  putative branch site (score: 3)
                             ttaaactagaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtattattttaataaaccatggtgtttttattgtcgagctacggtttctgctttgtggtatgttccaatccttaaactagaattaattgtgctttagGTTTTGAGAAGCCATCTGCCATTCAGCAAAGGGGGATAGTTCCCTTCTGCAAGGGACTTGATGTTATTCAGCAGGCTCAGTCTGGAACTGGGAAGACGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - -ccatggt
- - - - - - - - - - - - - - - - - - - - gctacgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatcc