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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttatgaattctaaccatcgctacagtttggaacttatttacaaatgtgatattttgcgcagctgagatttttcttttaacttggcctgttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAAGATCTGGGACAGATGGACGTGGATGCATCTGATGAGTCAGCTAACATGC

Basic information

species Glycine max
transcript GLYMA08G18560.3
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|8827757|gb|BE211487.1|BE211487
EST:     GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|31305685|gb|CD390888.1|CD390888
EST:     CACCGTTCGGTGCTCCGCTGAATACGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: CACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|254324562|gb|GR833987.1|GR833987
EST:     GACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|192313316|gb|FK005088.1|FK005088
EST:     CACCGTTCGGTGCTCCGCTGAGTTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: CACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|4313320|gb|AI460439.1|AI460439
EST:     GAGACACCG-TCGGTGCTCCG-T-AATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|193376980|gb|FK340615.1|FK340615
EST:     GAGACACCGTTCGGTGCTCCGCTGAATACGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|27426337|gb|CA937857.1|CA937857
EST:     ACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: ACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|192313317|gb|FK005089.1|FK005089
EST:     CACCGTTCGGTGCTCCGCTGAGTTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: CACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|11412304|gb|BF424315.1|BF424315
EST:     GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|193713513|gb|FK654498.1|FK654498
EST:     GAGACACCGTTCGGTGCTCCGCTGAATACGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|6914757|gb|AW396287.1|AW396287
EST:     TTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: TTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|7639980|gb|AW734290.1|AW734290
EST:     GTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|254324561|gb|GR833986.1|GR833986
EST:     GACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|6914456|gb|AW395986.1|AW395986
EST:     GTTGTGGCCCCTGCGCTTCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|58014741|gb|CX701483.1|CX701483
EST:     GAGACACCGTTCGGTGTTCCGCTGAATTCGGTTGTGGCCCTTGCGTTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|4298166|gb|AI442722.1|AI442722
EST:     GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: GAGACACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
EST: gi|31472363|gb|CD414391.1|CD414391
EST:     CACCGTTCGGTGCTCCGCTGAATACGGTTGTGGCCCCTGCGCTCCG                         CTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA
genomic: CACCGTTCGGTGCTCCGCTGAATTCGGTTGTGGCCCCTGCGCTCCGgtgagtgact ... gttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgatattttgcgcagctgagatttttcttttaacttggcctgttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAAGATCTGGGACAGATGGACGTGGATGCATCTGATGAGTCAGCTAACATGC
                               ttttaac  putative branch site (score: 2)
                        atttttcttttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctttatgaattctaaccatcgctacagtttggaacttatttacaaatgtgatattttgcgcagctgagatttttcttttaacttggcctgttgttgcagCTGCAATTTTACACTCAAAAGGACCTCATGTCTAACATAGAGGAGAACAAAGATCTGGGACAGATGGACGTGGATGCATCTGATGAGTCAGCTAACATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT