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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatacaactacaactacgtcatggcttgatctttaaagccataactataccttttcttttttttcttttcaaaacaaaactataaacgtatgcatttctgaattaacattttcatctggaatctttctcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAAGCTATGAATATGCCCGAGGAACAAGCTGGCGGACAACCTGGTGCTCCGG

Basic information

species Glycine max
transcript GLYMA18G47920.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47920.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g00820.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtatacaactacaactacgtcatggcttgatctttaaagccataactataccttttcttttttttcttttcaaaacaaaactataaacgtatgcatttctgaattaacattttcatctggaatctttctcgatac---cagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAAGCTATGAATATGCCCGAGGAACAAGCTGGCGGACAACCTGGTGCTCCGG
                 | ||    | ||  |||   | |   || ||||  |    |||||| ||||  ||  |     | | | |   |     | | |||| ||| | |  ||   | |    |  ||||  |||    ||||||||||| |||||||| ||||||||||| || |||||||| || || |||||| |||| ||||| ||||| || |||   || || || ||  | |  |
--------------gtgagtattcaaaggagtgaa--taatttccgtaacc-tgttctttcttgttttgtttaactttgtagagccaagtaaaatagaacttctaaat-acctcttgtctttctttttcttctgtatatgttcagTGGATGTATCTGATCCCTCTTGGACTCATTGTCATGAATGCCGTAACCCAAGCTCTGAACATGCCTGAGGAGCAGGCTACTGGCCAGCCAGGCTCCCAAG
















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|208208298|gb|GE004257.1|GE004257
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|208303028|gb|GE100961.1|GE100961
EST:     TTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: TTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|254345763|gb|GR859410.1|GR859410
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|207757992|gb|GD727744.1|GD727744
EST:     GCCAATAGAAAGGTCCTTTTTTGGGTCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCA
genomic: GCCAATAGAAAGGTCC--TTTTGGG-CTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCA
EST: gi|193325160|gb|FK291410.1|FK291410
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTC
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTC
EST: gi|208059234|gb|GD859462.1|GD859462
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGAACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193532996|gb|FK488546.1|FK488546
EST:     TTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: TTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193591208|gb|FK546421.1|FK546421
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTG
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTG
EST: gi|193351792|gb|FK313833.1|FK313833
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193604754|gb|FK557745.1|FK557745
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGACGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|254331915|gb|GR843658.1|GR843658
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|207706648|gb|GD688596.1|GD688596
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|31463611|gb|CD405639.1|CD405639
EST:     TGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: TGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|208208470|gb|GE008461.1|GE008461
EST:     GAGGCGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|208302857|gb|GE099152.1|GE099152
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|9985624|gb|BE659732.1|BE659732
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|208152618|gb|GD949121.1|GD949121
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193710684|gb|FK647736.1|FK647736
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGAGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193318100|gb|FK286224.1|FK286224
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193380905|gb|FK348792.1|FK348792
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|254345762|gb|GR859409.1|GR859409
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|208172852|gb|GD972059.1|GD972059
EST:     GCCAATAGAAAGGTCCTTTTGGGTCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCA
genomic: GCCAATAGAAAGGTCCTTTTGGG-CTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCA
EST: gi|193480499|gb|FK444721.1|FK444721
EST:     AAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: AAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193340217|gb|FK307838.1|FK307838
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|193442901|gb|FK404251.1|FK404251
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTT-GGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|207702293|gb|GD683048.1|GD683048
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCC
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCC
EST: gi|193661306|gb|FK600916.1|FK600916
EST:     TTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: TTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|207782115|gb|GD753686.1|GD753686
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|6095030|gb|AW119697.1|AW119697
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
EST: gi|208256364|gb|GE051747.1|GE051747
EST:     GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC                         TGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA
genomic: GAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATACgtgagtatac ... tcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacgtatgcatttctgaattaacattttcatctggaatctttctcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAAGCTATGAATATGCCCGAGGAACAAGCTGGCGGACAACCTGGTGCTCCGG
                  aattaac  putative branch site (score: 2)
                                       tctttctc  putative PPT
                  aattaacattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatacaactacaactacgtcatggcttgatctttaaagccataactataccttttcttttttttcttttcaaaacaaaactataaacgtatgcatttctgaattaacattttcatctggaatctttctcgataccagTGGATGTACCTGATCCCGCTTGGACTCATAGTAATGAATGCTGTTACTCAAGCTATGAATATGCCCGAGGAACAAGCTGGCGGACAACCTGGTGCTCCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG