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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacaaatttctctgctgttggtttggttttttattgctgatgctggagtttgtatctacttgtattataactttttttttgtcttattgacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG

Basic information

species Glycine max
transcript GLYMA03G34540.1
intron # 3
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|37997616|gb|CF809205.1|CF809205
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|58015690|gb|CX702432.1|CX702432
EST:     AGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: AGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|213610992|gb|DB970919.1|DB970919
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|10848192|gb|BF070735.1|BF070735
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCACGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|151395409|gb|EV265286.1|EV265286
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|5678132|gb|AI939262.1|AI939262
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|298167079|gb|HO010518.1|HO010518
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|254348136|gb|GR851815.1|GR851815
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|27427318|gb|CA938838.1|CA938838
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
EST: gi|192328158|gb|FK020419.1|FK020419
EST:     CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAAT                         CTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
genomic: CGTATCAACAGTTTTTGCATTCGCTTGATCAGGTCAAGATTCAAAATAATgtaagtttca ... gacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagtttgtatctacttgtattataactttttttttgtcttattgacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG
                                         tattgac  putative branch site (score: 2)
                ttgtattataactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacaaatttctctgctgttggtttggttttttattgctgatgctggagtttgtatctacttgtattataactttttttttgtcttattgacttgtcagCTGAAAGATGAACTTTGCAAGGAGAATTTACAGCTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
catacaa
- - - - - -ctctgct
- - - - - - - - - - -ggtttgg
- - - - - - - - - - - - - - - - - - - ctgatgc
- - - - - - - - - - - - - - - - - - - - - - - -gagtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacttg