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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgattatacttacatagtaaagtataagaattgactgtaatttctgtaaaaaaaaattacttgcaacaccctatatgttgcacttgatgatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGACTCTCGGAATCCGTCAAATTCGTCCACGAAGTGGGACCTACAGCTGAAA

Basic information

species Glycine max
transcript GLYMA15G23150.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G23150.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g03950.t01 (Vitis vinifera), 3'ss of exon 8
-----aatgattatacttacatagtaaagtataagaattgactgtaatttctgtaaaaaaaaattacttgcaacaccctatatgttgcacttgatgatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGACTCTCGGAATCCGTCAAATTCGTCCACGAAGTGGGACCTACAGCTGAAA
     | ||  || |  | |||   |   |     |||   |    ||  |            ||  ||   | |  ||| || |      || |     ||||||||||| ||||| ||||||| || |||||  ||| |||||| || ||||| ||||| |||||  ||||| | ||||| ||| ||||| || |||||||||
tatagattgcctacatcttcatgaaatcatcctt-aatcacccagcatccccccggtt---ttttttttctcataaactaaat-tgaagtctgttcgatcttcagCTGCAGTTGCAACGGAATGAAGTGATTGCCCTGATGAACCTACTCAATCGGCTCTCAGAATCACTCAAAGTTGTCCATGAAATGGGAACTTCAGCTGAAA
















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|254332820|gb|GR850070.1|GR850070
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
EST: gi|58023979|gb|CX710720.1|CX710720
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
EST: gi|15815000|gb|BI787275.1|BI787275
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAGGAAT
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAAT
EST: gi|254332819|gb|GR850069.1|GR850069
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
EST: gi|6914968|gb|AW396498.1|AW396498
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAAGAATGAGGTAATTGCATTGACGAACCTTCCTAATCGA
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
EST: gi|58024165|gb|CX710906.1|CX710906
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
EST: gi|57575810|gb|CX548781.1|CX548781
EST:     CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACA                         CTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA
genomic: CATTAAAGATTCTCTTCTCTGTTGATGGTCAAGAAAACTCGAGTCATACAgtaagtacat ... gatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaaaaaaaaattacttgcaacaccctatatgttgcacttgatgatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGACTCTCGGAATCCGTCAAATTCGTCCACGAAGTGGGACCTACAGCTGAAA
                                      acttgat  putative branch site (score: 5)
                                               tctttc  putative PPT
     aaaaaaaattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgattatacttacatagtaaagtataagaattgactgtaatttctgtaaaaaaaaattacttgcaacaccctatatgttgcacttgatgatctttcagCTGCAGCTGCAAAGGAATGAGGTAATTGCATTGACGAACCTTCTTAATCGACTCTCGGAATCCGTCAAATTCGTCCACGAAGTGGGACCTACAGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactt