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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactcatcatgacggtacatatagtctttacttcttttgcaaaagattttgtattaatttccaaatataattttttggatatgtatgcataattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG

Basic information

species Glycine max
transcript GLYMA13G39990.1
intron # 13
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|31464325|gb|CD406353.1|CD406353
EST:     TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG                         GGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
genomic: TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatc ... taattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
EST: gi|209728921|gb|BW654988.1|BW654988
EST:     TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG                         GGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
genomic: TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatc ... taattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
EST: gi|20449491|gb|BQ253615.1|BQ253615
EST:     TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG                         GGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
genomic: TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatc ... taattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
EST: gi|12691502|gb|BG157838.1|BG157838
EST:     TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG                         GGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCT
genomic: TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatc ... taattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
EST: gi|10233381|gb|BE802269.1|BE802269
EST:     TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG                         GGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
genomic: TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatc ... taattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
EST: gi|10234562|gb|BE803450.1|BE803450
EST:     TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG                         GGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
genomic: TTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAGgttagacatc ... taattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttgtattaatttccaaatataattttttggatatgtatgcataattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG
       tattaat  putative branch site (score: 2)
 ttttc  putative PPT
 tattaatttccaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactcatcatgacggtacatatagtctttacttcttttgcaaaagattttgtattaatttccaaatataattttttggatatgtatgcataattttcagGGAGAGTCTGACAAAGGAAAAGGGCCAAGGGATTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
ctactca
- - - -tcatgac
- - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgca