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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagttagaccatattgattcagcatttgttatttttttttattagatttgacacgtaaaattagttattgactactttttggaggacatcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGGCAG

Basic information

species Glycine max
transcript GLYMA07G08030.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------------------------tgtagttagaccat-attgattca---gcatttgttatttttttttattagatttgacac-gtaaaattagttattgactactttt--tggaggacatcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGGCAG
                                               || ||   | || || ||  ||   | |  |   |  || | |  ||        ||    ||       |  |||  | ||||  ||   ||  |  ||| |||||||||||| ||||   |||||| || |||||||||||||| |||||||| |||
gtaggaatcttaatgattcaaatatagaatttacctctattaggcaataatttatcaatcatggaaccacttgtagctcacacattctctagttgaggaaatcattacaaggccgactgatgagaatttttcttgtctgattttatttgcagACAGATGATTTGCAGGGTCACATAATTATTTGTGGATTTGGTCGAGTTGGTCAG

upper sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 12
tgtagttagaccatattgattcagcatttgttatttttttt-tattagatttgacacgtaaaa-ttagttattgactactttttggaggacatcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGGCAG
  |  |   |  ||||    |      ||   |      || || | |  | |  ||  |    ||   | |||| | | | ||| | ||  |  ||| |||||||||||| ||||| |||| || || |||||||||||||| || ||||| |||
--tgatggaaagatatgttctgtatggttaacaccaagattatactggtgtagttactgatttctttaatcttgatttcctattgcatgattttgtttccagACAGATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGACAG
















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|16104878|gb|BI892618.1|BI892618
EST:     GTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAG                         ACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
genomic: GTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAGgtaagatcac ... tcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
EST: gi|10235459|gb|BE804347.1|BE804347
EST:     CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAG                         ACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
genomic: CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAGgtaagatcac ... tcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
EST: gi|22540098|gb|BU089941.1|BU089941
EST:     CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAG                         ACAGATGATCTGCAAATTCACATCATAATTTGTGGATCTGGGCGAGATGGG
genomic: CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAGgtaagatcac ... tcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
EST: gi|20498319|gb|BQ273249.1|BQ273249
EST:     CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAG                         ACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
genomic: CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAGgtaagatcac ... tcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
EST: gi|8669480|gb|BE190587.1|BE190587
EST:     CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAG                         ACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG
genomic: CCCGTTTTGAGCTGCATGATGTTCGAAGTTTATTGCCTGTGGAAAGTGAGgtaagatcac ... tcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttgacacgtaaaattagttattgactactttttggaggacatcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGGCAG
                      tattgac  putative branch site (score: 2)
                                           catctttt  putative PPT
            taaaattagttattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagttagaccatattgattcagcatttgttatttttttttattagatttgacacgtaaaattagttattgactactttttggaggacatcttttacagACAGATGATCTGCAAAATCACATCATAATTTGTGGATTTGGGCGAGTTGGGCAG

- - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - tgacacg