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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatgttccttattttattttccattcattgttattatacatacataacataacatgccaataagtcctaatttgtttatttaacatgccaataagagcttcatatgccttttcatcatacaataaccaaaggctaagtttagttctgtgttcttttttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAAGATCAAAATGGCTACATATCAGCTAGTGAG

Basic information

species Glycine max
transcript GLYMA20G35440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35440.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g04420.t01 (Vitis vinifera), 3'ss of exon 2
gtaaattatgttccttattttattttccattcattgttattatacatacataacataacatgccaataagtcctaatttgtttatttaacatgccaataaga-gcttcatatgccttttcatcatacaataaccaaaggctaagtttagttctgtgttcttttttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAAGATCAAAATGGCTACATATCAGCTAGTGAG
                                          || |   |||   | |  |   |   |  |  |||    ||||    | | | | | | | |||    |||  | |  |    ||  |   | |||   | || |   | | | |||||  || ||  |||| || || ||||| |||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| | ||||
-----------------------------------------gtataataatattttgaactatgatctatacggaatagccttatgcctcttacaatttaaatgctcagcatgt-tataaacttcaccgtcgactaag---atgtctgtgtttttcttcttggttaacc-agGAAACAGACGCAGAAGAGGAGCTTAAAGAAGCCTTCAAAGTTTTTGACAAGGATCAAAATGGTTACATCTCAGCCACTGAG
















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|151398604|gb|EV268475.1|EV268475
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|10252591|gb|BE820357.1|BE820357
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|192329953|gb|FK021539.1|FK021539
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTCTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|192334235|gb|FK026616.1|FK026616
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|192329952|gb|FK021538.1|FK021538
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTCTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|192334236|gb|FK026617.1|FK026617
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|192311224|gb|FK003737.1|FK003737
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|192311223|gb|FK003736.1|FK003736
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|15000001|gb|BI320815.1|BI320815
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|7589101|gb|AW704882.1|AW704882
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|151411418|gb|EV281229.1|EV281229
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|19270785|gb|BM887041.1|BM887041
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
EST: gi|7028648|gb|AW458431.1|AW458431
EST:     GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAA                         GACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA
genomic: GAACCATTGAATTCGATGAGTTCTTGAGCTTGATGGCCAAGAAAGTGAAAgtaaattatg ... tttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatcatacaataaccaaaggctaagtttagttctgtgttcttttttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAAGATCAAAATGGCTACATATCAGCTAGTGAG
         caataac  putative branch site (score: 2)
                                ttctgtgttctttttt  putative PPT
      atacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatgttccttattttattttccattcattgttattatacatacataacataacatgccaataagtcctaatttgtttatttaacatgccaataagagcttcatatgccttttcatcatacaataaccaaaggctaagtttagttctgtgttcttttttcacttagGACACCGATGCAGAGGAGGAGCTCAAAGAGGCTTTCAAGGTTTTTGACAAAGATCAAAATGGCTACATATCAGCTAGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT