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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttggggctgtggtttaatggggttcggttgttagaagcaatcattgagtttttggctctgatggggttttggggggaaattgtttctttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG

Basic information

species Glycine max
transcript GLYMA10G35230.2
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|5605755|gb|AI899819.1|AI899819
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|151394915|gb|EV264786.1|EV264786
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|193724791|gb|FK658075.1|FK658075
EST:     TCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: TCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|15813084|gb|BI785359.1|BI785359
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|308098577|gb|HO760318.1|HO760318
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|298165609|gb|HO011658.1|HO011658
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|298182667|gb|HO031402.1|HO031402
EST:     ACTTCCAAACT-TTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: ACTTCCAAA-TCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|298183380|gb|HO028593.1|HO028593
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|192326781|gb|FK018908.1|FK018908
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|7286166|gb|AW598653.1|AW598653
EST:     GCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: GCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|298177777|gb|HO027330.1|HO027330
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|151411846|gb|EV281657.1|EV281657
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|193481083|gb|FK444788.1|FK444788
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCA
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCA
EST: gi|298185154|gb|HO030367.1|HO030367
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|298174351|gb|HO017687.1|HO017687
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGTGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGAC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
EST: gi|192296028|gb|FG989422.1|FG989422
EST:     CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAG                         ATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC
genomic: CACTTCCAAATCTTCTCCTCTCGCTATGGGTTGCGGCTCCTCCCTTCCAGgtaatcatat ... ttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgagtttttggctctgatggggttttggggggaaattgtttctttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG
             ctctgat  putative branch site (score: 4)
                                     ttgtttctttgttt  putative PPT
                                  aaattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttggggctgtggtttaatggggttcggttgttagaagcaatcattgagtttttggctctgatggggttttggggggaaattgtttctttgtttgcagATAGGGGCTCAAGGCAGTTGGGTCGACCCAATTCAGAGAATGGTGGAGGGCAGGACGCCAAGAATCTGAGGGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG