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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgttcggaatatgtggaattgagctctgattttagcctacctttgttcttaattaatgtaaaattaaccttgcgattcgttatgttatttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTACGGATCTAGAAGGCTATTTAGCAGTGGTTCTGGAAAAATACTGAGCGAGGA

Basic information

species Glycine max
transcript GLYMA12G09600.2
intron # 1
splice site 3'
intron type U2

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|5126760|gb|AI748496.1|AI748496
EST:     CTCCACTGAACTGAGTCTGAAG                       
genomic: CTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacaga
EST: gi|33388268|gb|CA851475.1|CA851475
EST:     CATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGANCTGAGNNTGAAG                         AGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTAC
genomic: CATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAG--T-CTGgtaatttatt ... tttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTAC
EST: gi|151411066|gb|EV280877.1|EV280877
EST:     CATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACCGAGTCTGAAG                         AGGGAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTAC
genomic: CATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTAC
EST: gi|151398999|gb|EV268870.1|EV268870
EST:     ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCTGAAG                       
genomic: ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacaga
EST: gi|10253437|gb|BE821203.1|BE821203
EST:     CTCCACTGAACTGAGNCTGAAG                         AGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTAC
genomic: CTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTAC
EST: gi|192301404|gb|FG998396.1|FG998396
EST:     ACACATTGCTTCTGCTAACCCTCTCTGGGTTCTCCACTGAACTGAGTCTGAAG                       
genomic: ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacaga
EST: gi|151412650|gb|EV282462.1|EV282462
EST:     ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCTG                         AGGAAAACATTTAACTAACTGCAATAGCTGCACGTGTGGCTGCAAGGTACG
genomic: ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCTGgtaatttatt ... tttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTACG
EST: gi|16346323|gb|BI971918.1|BI971918
EST:     CCCTCTCTGGGCTCTCCACTGAACTGAGTCTGAAG                       
genomic: CCCTCTCTGGGCTCTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacaga
EST: gi|192326512|gb|FK018819.1|FK018819
EST:     ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCTGAAG                       
genomic: ACACATTGCTTCTGCTAACCCTCTCTGGGCTCTCCACTGAACTGAGTCT---Ggtaatttatt ... tttacaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcttaattaatgtaaaattaaccttgcgattcgttatgttatttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTACGGATCTAGAAGGCTATTTAGCAGTGGTTCTGGAAAAATACTGAGCGAGGA
                   aattaac  putative branch site (score: 2)
      ttaattaatgtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgttcggaatatgtggaattgagctctgattttagcctacctttgttcttaattaatgtaaaattaaccttgcgattcgttatgttatttacagaagAGGAAAACATTTAACTAACTGCAATGGCTGCACGTGTGGCTGCAAGGTACGGATCTAGAAGGCTATTTAGCAGTGGTTCTGGAAAAATACTGAGCGAGGA

-agtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accttgc