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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgcatgtcttttctcttttgattattttctattgactaaaactttctttagatagagattgatttttatttttttataatcattattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAACTA

Basic information

species Glycine max
transcript GLYMA16G17150.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17150.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 8
gtacttgcatgtcttttctcttttgattattttc-tattgactaaaactttctttagata---gaga----ttgatttttatttttttataatcattattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAACTA
|||    ||| |    |   ||| | || ||||| || |   ||    |||   | || |   ||||     |  || | | ||||||   |  | |  |  |||| |||||||||||| ||||| |||||||||||||||   | || || |   | 
gtagcaacatattcccttattttggttttttttcatacttcatactgattttcatggagaaatgagagcttctagttctgaattttttggtaaaactggtgcagGGATCAGCAAAGAATCTGCCCCCATCCTGCACTTCAAGTCTAAGACCGGGCTTG
















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|6070525|gb|AW099912.1|AW099912
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|7590021|gb|AW705783.1|AW705783
EST:     CANGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAGAGAATTTGCCCTCATCCTGCACTTCAAAATTCAACCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6666292|gb|AW277751.1|AW277751
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6668069|gb|AW279520.1|AW279520
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|7589651|gb|AW705421.1|AW705421
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6667401|gb|AW278852.1|AW278852
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6455714|gb|AW186397.1|AW186397
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGGAGTTGTTTCAACTCAT                         GGCTCAGCCAAGGATTTGCCCTCATCCTGCACT
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACT
EST: gi|6724652|gb|AW309107.1|AW309107
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6667540|gb|AW278991.1|AW278991
EST:     TGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: TGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|151395749|gb|EV265626.1|EV265626
EST:     CACGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAA
EST: gi|151394400|gb|EV264271.1|EV264271
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6455546|gb|AW186229.1|AW186229
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6455060|gb|AW185743.1|AW185743
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6668142|gb|AW279593.1|AW279593
EST:     CATGAACACATTTCATCGAGGAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAGAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|10255077|gb|BE822843.1|BE822843
EST:     AGTGAAGTTGTTTCANNNCAT                         NNCTCAGCAAAGAATTTGCNNNCATNNNGCACTTCAAAATTCAGCCCAGAA
genomic: AGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|7589195|gb|AW704974.1|AW704974
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|298163578|gb|HO012311.1|HO012311
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|5753462|gb|AI960749.1|AI960749
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
EST: gi|6341492|gb|AW164316.1|AW164316
EST:     CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCAT                         GGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA
genomic: CAGGAACACATTTCATCGAAAAGTTCTACAGTGAAGTTGTTTCAACTCATgtacttgcat ... attattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaactttctttagatagagattgatttttatttttttataatcattattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAACTA
                    gattgat  putative branch site (score: 4)
               atagagattgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgcatgtcttttctcttttgattattttctattgactaaaactttctttagatagagattgatttttatttttttataatcattattatagGGCTCAGCAAAGAATTTGCCCTCATCCTGCACTTCAAAATTCAGCCCAGAACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA