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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaataaaaataaaatttcctgtcatagtttaccagtttatgctaaatatggttcatgcctttattggtatgaagagtaactctttcttgtctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAGCAACGTGCTTATGAATTGCAAGCCTTTATAGGTTTGGATGTACAAGCTG

Basic information

species Glycine max
transcript GLYMA09G35240.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G35240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G31730.1 (Arabidopsis thaliana), 3'ss of exon 8
aaataaaaataaaatttcctgtcatagtttaccagtttatgctaaatatggttcatgcctttattggtatgaagagtaactctttcttgtctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAGCAACGTGCTTATGAATTGCAAGCCTTTATAGGTTTGGATGTACAAGCTG
           |  | || |   |  ||     |||  |    |||     |  ||  | |   |  |     || | |||  || |    || ||| |||||||||| |||||||||||  ||||||| || || ||  ||||||| ||||||||||| |||||  | || ||  |  | | | | ||||  |  ||||
---------gtatgtatctttagacggtcctgaagtgaa----aaaccaaatctatagcct-gctttttcacggactgactggtttt---ata-ttgtagTGCCAATCTTTGATTGAAGAGCTATTGGCTTCACATTCAACAGATCTTCAGCAACGTGCATATGAGCTTCAGGCTCTCCTTGCTCTAGATGCCCGTGCTG

upper sequence: GLYMA09G35240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 3'ss of exon 9
aaataaaaataaaatttcctgtcatagtttacc----agtttatgctaaatatggttcatgcctttattggtatgaagagtaactctttcttgtctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAGCAACGTGCTTATGAATTGCAAGCCTTTATAGGTTTGGATGTACAAGCTG
||  |||| |  || |   | | ||    |  |    || | ||||    |||  |   |   | ||| |||||  |  ||||  |||| || |||  |||||||| ||||| ||||| |||||| |||  |||||||||||  ||||| | || || ||||| ||||||||||||||  || |     | ||||  || ||||
aatgaaaattggaactcatttttatgaaatttcgtaaagctcatgcaggttata-tgtgtaa-tctatgggtatcta--gtaatcctttgttctcttgttgcagTGTCAATCCTTGATCGAAGAACTATCAGCATCCCACTCAACAGATTTACAACAGCGTGCCTATGAATTGCAAGCAGTTGTCACCCTAGATGCTCATGCTG
















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|23734961|gb|BU765740.1|BU765740
EST:     TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAG                         TGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
genomic: TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAGgtatatgctg ... ctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
EST: gi|9901369|gb|BE610337.1|BE610337
EST:     TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAG                         TGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
genomic: TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAGgtatatgctg ... ctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
EST: gi|208279564|gb|GE073687.1|GE073687
EST:     TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAG                         TGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
genomic: TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAGgtatatgctg ... ctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
EST: gi|213608293|gb|DB972635.1|DB972635
EST:     TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAG                         TGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
genomic: TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAGgtatatgctg ... ctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
EST: gi|254346448|gb|GR856170.1|GR856170
EST:     TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAG                         TGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG
genomic: TTTATGCATTTGAAGTAGCAGCCGGGAGGAAAGTGGATATCCTATCTGAGgtatatgctg ... ctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatggttcatgcctttattggtatgaagagtaactctttcttgtctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAGCAACGTGCTTATGAATTGCAAGCCTTTATAGGTTTGGATGTACAAGCTG
                            gagtaac  putative branch site (score: 2)
                                  ctctttcttgtctact  CT-rich tract
              tttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataaaaataaaatttcctgtcatagtttaccagtttatgctaaatatggttcatgcctttattggtatgaagagtaactctttcttgtctacttgcagTGCCAATCGTTGATTGAAGAATTATTGGCATCCCACTCTTCAGATCTGCAGCAACGTGCTTATGAATTGCAAGCCTTTATAGGTTTGGATGTACAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - -aaaataa
- - - - - - - - -cctgtca
- - - - - - - - - - - - - - - - - -tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatga