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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtggctatttatgttccccgggtttctggtctgactgggcggactggtccattttttagtcactggttatgatttcaatgattttgtcgaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAAGCCAGCAG

Basic information

species Glycine max
transcript GLYMA07G40350.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 5
ttgtggctatttatgttccccgggtttctggtctgactgggcggactggtccattttttagtcactggttatgatttcaatgattttgtcgaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAAGCCAGCAG
  || |   |||||  |    |   |  || |             || |   || |  || ||| |  |||  || |   |  |||  |   || | |||||||||||||| ||||| |||||  | ||||||||||| ||| | ||||||||||||||
--gtaggactttatcataattg--ctattgtttcatgcatcatttcttgcaaatgtgataatca-tatttagaatgtttttcttttcat--gattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG
















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|151398252|gb|EV268130.1|EV268130
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|31469040|gb|CD411068.1|CD411068
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|15664820|gb|BI702191.1|BI702191
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAANAGCCCCATAATGATCATCTACCCTCTA-TAGA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACC-TCTAATAGA
EST: gi|31466950|gb|CD408978.1|CD408978
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|21256394|gb|BQ453282.1|BQ453282
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|19348270|gb|BM892802.1|BM892802
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|207799176|gb|GD768203.1|GD768203
EST:     CTCAAAGTTTATGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTAGAAAAATGTCAATAAGAAAAAGCCCCATAATG
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGT-GAAAAATGTCA-TA-GAAAA-GCCCCATAATG
EST: gi|207709086|gb|GD692196.1|GD692196
EST:     CTCAAAGTTTATGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATG
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATG
EST: gi|26048289|gb|CA784806.1|CA784806
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|22928767|gb|BU545906.1|BU545906
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|31463603|gb|CD405631.1|CD405631
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCCAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
EST: gi|9902296|gb|BE611264.1|BE611264
EST:     CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAA                         GTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA
genomic: CTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggttta ... gaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtccattttttagtcactggttatgatttcaatgattttgtcgaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAAGCCAGCAG
                            atttcaatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtggctatttatgttccccgggtttctggtctgactgggcggactggtccattttttagtcactggttatgatttcaatgattttgtcgaatatgcagGTGAAAAATGTCATAGAAAAGCCCCATAATGATCATCTACCTCTAATAGAAGCCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC