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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatctttataggagatttctgggattactaatgggagaatttattagtgtctattgtatagatttaaccatctgattgcctttatttgtgccatatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGGATCCTCTAGCGGAGCAAAGAAGGCATTTACTGGAATGTGAAATTTGAAT

Basic information

species Glycine max
transcript GLYMA09G12420.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G12420.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 5
gttagatctttataggagatttc-------tgggattactaatgggaga---atttat----tagtgtctattgtatagatt--taaccatctgattgcctttatttgtgccata--tgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGGATCCTCTAGCGGAGC---AAAGAAGGCATTTACTGGAATGTGAAATTTGAAT
  || ||||| |   || | | |       | |   | | |||   |     |||||     | |||     ||| |   ||  | | |||    |||  | | | | |    |   | || |||||| | || |||||||| |||||||| ||||| ||||||||||| |||||||| ||| | ||||     |||||||| ||||||| |||||||| ||||   
-gtaaatcttcaattgaaactacctccagtttgtccttccaataaaaagttgatttagagggtggtgaactctgtgtttgttactgaacataatgttgtttctttctatattttccttattcagGCCACTATCAAAGACAGTAAGGTTCAACGTTTTGAAAGTGATTCCTGCTGGATCTTCTGGTGGAGGTGGGAAGAAGGCTTTTACTGCAATGTGAAGTTTG---
















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|192295631|gb|FG990485.1|FG990485
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|192327596|gb|FK020643.1|FK020643
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|213610237|gb|DB980823.1|DB980823
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|31474232|gb|CD416260.1|CD416260
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCTATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|298193555|gb|HO040203.1|HO040203
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAATGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|213612020|gb|DB964856.1|DB964856
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGAT
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGAT
EST: gi|151409325|gb|EV279133.1|EV279133
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|192334070|gb|FK026227.1|FK026227
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATTTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|298192237|gb|HO036319.1|HO036319
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTT
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTT
EST: gi|192329280|gb|FK020199.1|FK020199
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|192323316|gb|FK017422.1|FK017422
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|10256428|gb|BE824194.1|BE824194
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|151410570|gb|EV280385.1|EV280385
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|38192824|gb|CF922030.1|CF922030
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|192327595|gb|FK020642.1|FK020642
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|38193079|gb|CF922285.1|CF922285
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|298185805|gb|HO030966.1|HO030966
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGT
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGT
EST: gi|151412049|gb|EV281861.1|EV281861
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|213610749|gb|DB963135.1|DB963135
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|192334069|gb|FK026226.1|FK026226
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|18040050|gb|BM308344.1|BM308344
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
EST: gi|208160000|gb|GD955692.1|GD955692
EST:     CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAG                         GCCAATCTCAAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG
genomic: CCTTGTTTCCGTGTTAAAGAAGGAGATCATGTTATTATTGGCCAATGCAGgttagatctt ... atatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctattgtatagatttaaccatctgattgcctttatttgtgccatatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGGATCCTCTAGCGGAGCAAAGAAGGCATTTACTGGAATGTGAAATTTGAAT
     attgtatagatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatctttataggagatttctgggattactaatgggagaatttattagtgtctattgtatagatttaaccatctgattgcctttatttgtgccatatgtttagGCCAATCTCGAAGACAGTGAGGTTCAATGTTTTAAAAGTGATTCCAGCTGGATCCTCTAGCGGAGCAAAGAAGGCATTTACTGGAATGTGAAATTTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG