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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatttgaagcttttttccaatctttgcattttggtccattggtgggctgtttgacattgtgtagttgctaaccatctgtgtggctttctcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTGGGGATCCCGCTGGAGTGCATAAGGCATTAGAGTTAATTGCCTCCCACCT

Basic information

species Glycine max
transcript GLYMA03G40840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40840.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0081g00440.t01 (Vitis vinifera), 3'ss of exon 4
aaaatttgaagcttttttccaatctttgcattttggt----ccattggtgg--gctgtttgacattgtgtagttgctaaccatctgtgtggctttctcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTGGGGATCCCGCTGGAGTGCATAAGGCATTAGAGTTAATTGCCTCCCACCT
     | ||  | ||| |  ||||||    ||||| |    |   | || |  || || | |  |||  ||| |  ||||      | |    |    |  |||||||||||| || |||||||| || |||||||| ||||| ||||||||||| ||||| |||  |||||||||||| ||| | ||| ||||||| || |||||
-----tagattcatttcttaaatcttgtgcttttgttacttctgcttgtagctgcagtataat-ttgcataggtcttaactccaattttaaaatgaattgttgcagAAGACCTACCCATTTTTGCACTCCAAGATGATAGGGTTGTTGAAGTAGTAGGGGAACCCATTGGAGTGCATAAAGCAGTGGAGCTAATTGCATCTCACCT
















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|8283100|gb|BE020669.1|BE020669
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|193670458|gb|FK611560.1|FK611560
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTAG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|193650907|gb|FK598522.1|FK598522
EST:     CCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: CCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|192331608|gb|FK019969.1|FK019969
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|6666253|gb|AW277712.1|AW277712
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGGTCTTGGAGCAA                         AAGACCTCCCT
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCT
EST: gi|208188084|gb|GD986898.1|GD986898
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|254332498|gb|GR846436.1|GR846436
EST:     AAAATCTATCCCAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGG-TGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|193606984|gb|FK560005.1|FK560005
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|192328162|gb|FK020423.1|FK020423
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|193555319|gb|FK511018.1|FK511018
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|193643760|gb|FK589491.1|FK589491
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTT-GCCCTTCAAG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAG
EST: gi|208296550|gb|GE090140.1|GE090140
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAAGACCTACCCTAATTTTTAGACCCTTCAAGATGAC
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAA-GACCT-CCCTA-TTTTT-G-CCCTTCAAGATGAC
EST: gi|15661574|gb|BI698945.1|BI698945
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
EST: gi|298183659|gb|HO028872.1|HO028872
EST:     AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAG                         AAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG
genomic: AAAATCTATCCAAGAAGCATCCAATTGTATTGTTAGAGTTCTTGGAGCAGgttcttgcta ... tcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggctgtttgacattgtgtagttgctaaccatctgtgtggctttctcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTGGGGATCCCGCTGGAGTGCATAAGGCATTAGAGTTAATTGCCTCCCACCT
                      tgctaac  putative branch site (score: 1)
                                        ctttctcttctgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatttgaagcttttttccaatctttgcattttggtccattggtgggctgtttgacattgtgtagttgctaaccatctgtgtggctttctcttctgcagAAGACCTCCCTATTTTTGCCCTTCAAGATGACAGGGTGGTTGAAGTAGTTGGGGATCCCGCTGGAGTGCATAAGGCATTAGAGTTAATTGCCTCCCACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - - - -tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgtgg