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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattttggggttgtggtttaatggggttcggttgttagaagcaatcattgagttttggctctgatggggttttggggggaaattgttttttggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG

Basic information

species Glycine max
transcript GLYMA20G32320.1
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|208146931|gb|GD950576.1|GD950576
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|298188274|gb|HO034967.1|HO034967
EST:     ACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: ACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|207710286|gb|GD689752.1|GD689752
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAAT
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAAT
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|14009240|gb|BG725844.1|BG725844
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|21887641|gb|BQ740854.1|BQ740854
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|120530730|gb|EH258863.1|EH258863
EST:     ACTTCCAAATTCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCNCAATTCCGAGAATGGTGGAGG
genomic: ACTTCCAAA-TCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGA-CC-CAATTCCGAGAATGGTGGAGG
EST: gi|33388034|gb|CA851241.1|CA851241
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|120530900|gb|EH259033.1|EH259033
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|213603351|gb|DB966610.1|DB966610
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|14126037|gb|BG790475.1|BG790475
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|11687687|gb|BF595363.1|BF595363
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     TCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: TCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|151409251|gb|EV279059.1|EV279059
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|192303625|gb|FG998635.1|FG998635
EST:     CACTTCCAAATCTTCTCCCCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|151399728|gb|EV269599.1|EV269599
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|19053755|gb|BM732422.1|BM732422
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|6912828|gb|AW394312.1|AW394312
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|6665996|gb|AW277455.1|AW277455
EST:     TCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: TCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
EST: gi|6455577|gb|AW186260.1|AW186260
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAGgtaatcatat ... tggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgagttttggctctgatggggttttggggggaaattgttttttggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG
             ctctgat  putative branch site (score: 4)
                                     ttgtttttt  putative PPT
                                  aaattgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattttggggttgtggtttaatggggttcggttgttagaagcaatcattgagttttggctctgatggggttttggggggaaattgttttttggtttgcagATAGGGATTCAAGGCAGTTGGGTCGACCCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - -tggggtt
- - - - ggttgtg
- - - - - - - - - - - - - - -ggttgtt
- - - - - - - - - - - - - - - - - - - - gcaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggggg