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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgattgtttattgtttaaattgttttatctgtatcaatcacattcttgttgctgttatatattataaagctattcaatgaatctgggttattaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGGCTAAAGAAATTGACTTATACTCAACAAATCAAGACTGCATCAAGATGCT

Basic information

species Glycine max
transcript GLYMA13G09260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G09260.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g15090.t01 (Vitis vinifera), 3'ss of exon 4
gtgattgtttattgtttaaattgttttatctgtatcaatcacattct-tgttgc---tgttatatattataaagctattcaatgaatctgggttatta------atacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGGCTAAAGAAATTGACTTATACTCAACAAATCAAGACTGCATCAAGATGCT
         ||  || | |||| |||| |||   |   | | | ||    || |   | || |  | | |  |  | ||   | |   |  ||| ||        |||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||||||||||||||||||||| | ||||||||||||||||| ||||||||||||||
---------taaagtctgaattattttttcta-gttgctgatactccacatttcatgttttttccaatttgcaatttttgtgtaagcttaagttgttgtgtctggtacagTGTATGATGTAACACGGCGTGAAACATTTACAAATCTATCTGACATATGGGCTAAAGAAATTGACCTGTACTCAACAAATCAAGATTGCATCAAGATGCT
















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|12691494|gb|BG157830.1|BG157830
EST:     TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG                         TATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
genomic: TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGGgtatgttgta ... attaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
EST: gi|163928959|gb|EH038663.1|EH038663
EST:     TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG                         TATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
genomic: TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGGgtatgttgta ... attaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
EST: gi|151394671|gb|EV264542.1|EV264542
EST:     TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG                         TATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
genomic: TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGGgtatgttgta ... attaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
EST: gi|254322261|gb|GR837675.1|GR837675
EST:     TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG                         TATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
genomic: TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGGgtatgttgta ... attaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
EST: gi|207783131|gb|GD757152.1|GD757152
EST:     TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGG                         TATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG
genomic: TAGAACACTTACTAGTTCATATTACAGAGGAGCTCAAGGAATAATTATGGgtatgttgta ... attaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgttgctgttatatattataaagctattcaatgaatctgggttattaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGGCTAAAGAAATTGACTTATACTCAACAAATCAAGACTGCATCAAGATGCT
                                            tattaat  putative branch site (score: 2)
          ttatatattataaagc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgtttattgtttaaattgttttatctgtatcaatcacattcttgttgctgttatatattataaagctattcaatgaatctgggttattaatacagTATATGATGTAACGCGGCGGGAAACCTTTACAAATCTATCTGATATATGGGCTAAAGAAATTGACTTATACTCAACAAATCAAGACTGCATCAAGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
gtgattg
- - - - - - - - - - - - - - - - - -caatcac
- - - - - - - - - - - - - - - - - - - - - - - - - -gctgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgaa