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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggattttgtgtcattgatgtgaatgtctgtttgtaccattctaactgttaaccaaacacacacacacacactcatagcatctcaattctcatattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAGAAGGCAGAAGGTGTTGATTTATCAGGCTATGGATCATCCAAAGTGGTTC

Basic information

species Glycine max
transcript GLYMA03G40720.1
intron # 6
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|16995884|gb|BM085256.1|BM085256
EST:     ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAG                         GATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
genomic: ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgt ... catattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
EST: gi|207740310|gb|GD714248.1|GD714248
EST:     ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAG                         GATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
genomic: ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgt ... catattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
EST: gi|298178228|gb|HO023963.1|HO023963
EST:     ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAG                         GATGGGCTGAGAATTACATACTTTTG
genomic: ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgt ... catattgtagGATGGGCTGAGAATTACATACTTTTG
EST: gi|13788218|gb|BG650810.1|BG650810
EST:     ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAG                         GATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
genomic: ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgt ... catattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
EST: gi|20448810|gb|BQ252934.1|BQ252934
EST:     ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAG                         GATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
genomic: ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgt ... catattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
EST: gi|298167582|gb|HO012845.1|HO012845
EST:     ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAG                         GATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG
genomic: ATACATTAATCAAAGAGAAACTTGGCTGGGCTCCAACTATGAAGTTGAAGgtattattgt ... catattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttaaccaaacacacacacacacactcatagcatctcaattctcatattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAGAAGGCAGAAGGTGTTGATTTATCAGGCTATGGATCATCCAAAGTGGTTC
 tgttaac  putative branch site (score: 2)
                                         ttctcat  putative PPT
                                              atattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggattttgtgtcattgatgtgaatgtctgtttgtaccattctaactgttaaccaaacacacacacacacactcatagcatctcaattctcatattgtagGATGGGCTGAGAATTACATACTTTTGGATCAAAGAGCAGCTTGAGAAAGAGAAGGCAGAAGGTGTTGATTTATCAGGCTATGGATCATCCAAAGTGGTTC

- - ttttgtg
- - - - - - - -tgatgtg
- - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - ccattct
- - - - - - - - - - - - - - - - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaca