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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgtctatgtaagcaggtgttctgattgaattatcaatgctatttgtttctatcattattcttatatttttttacatgtcttattctgaactgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA

Basic information

species Glycine max
transcript GLYMA08G19640.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 5
atcgtctatgtaagcaggtgttctgattgaattatcaatgctatttgt--ttctatcattattcttatatttttttacatgtcttattctgaactgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA
 |    || | ||     | ||| ||||    |    ||| |||||||  |  || |  |||| ||   || || |   |   | ||    ||||  ||||||||||| |||||||||||||| |||| |||||||| |||||||  |||||  | || ||||| || || |||
-tttcataagcaaatttttcttcagattcttattaatatgatatttgtgttcttaactctattgttgc-ttgttctttgtacttcatgtgaaacttctccagAAATTCAGAAAGGAAGACATGAAACTTTCAGGAACTGAGGCATTCATGCGTCGGTCAAATTCTTTACAGAGA
















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|193373413|gb|FK342411.1|FK342411
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|208069167|gb|GD869117.1|GD869117
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|208113975|gb|GD909780.1|GD909780
EST:     GGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: GGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|208176632|gb|GD979105.1|GD979105
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|193532237|gb|FK491945.1|FK491945
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|208324334|gb|GE125691.1|GE125691
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|193413949|gb|FK376543.1|FK376543
EST:     TGGTTAATAGGAACAAAAGAATATTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|207805992|gb|GD778287.1|GD778287
EST:     GGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
genomic: GGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGA
EST: gi|208143447|gb|GD942465.1|GD942465
EST:     TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAG                         AAATTCCGAAAGGAAGACATG
genomic: TGGTTAATAGGAACAAAAGAATGTTGGGCCAGCTTTTGGGAACTCTCGAGgtatatgata ... actgttccagAAATTCCGAAAGGAAGACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctatcattattcttatatttttttacatgtcttattctgaactgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA
                                              ctgttcc  CT-rich tract
      tatcattattcttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgtctatgtaagcaggtgttctgattgaattatcaatgctatttgtttctatcattattcttatatttttttacatgtcttattctgaactgttccagAAATTCCGAAAGGAAGACATGCAACTCTCAGGAACAGAGGCATATATGCGAAGATCTAATTCCTTGCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG