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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaatcttgtgacctttgaattctgtagtgtaattttatgaatttgatattggtgatgagtaattttttgattaaatattggatgctgaatggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAGCAAGAAATCTGCAAACTCGCAAGCCTCAACGAAGGGTTCTACTGCACAG

Basic information

species Glycine max
transcript GLYMA01G39720.1
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|151393328|gb|EV263203.1|EV263203
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
EST: gi|193495206|gb|FK463190.1|FK463190
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
EST: gi|208269719|gb|GE072155.1|GE072155
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
EST: gi|193706160|gb|FK647576.1|FK647576
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATACCTACTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAAT-CCT-CTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACG
EST: gi|7685270|gb|AW755918.1|AW755918
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
EST: gi|192301066|gb|FG987991.1|FG987991
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATTCTCTGGAGAGGAAAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
EST: gi|208289796|gb|GE088888.1|GE088888
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAG
EST: gi|192296790|gb|FG993088.1|FG993088
EST:     CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAA                         TTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG
genomic: CAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTCAGCACAAgtaatattat ... atggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatattggtgatgagtaattttttgattaaatattggatgctgaatggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAGCAAGAAATCTGCAAACTCGCAAGCCTCAACGAAGGGTTCTACTGCACAG
                     ttttgat  putative branch site (score: 4)
         tgatgagtaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaatcttgtgacctttgaattctgtagtgtaattttatgaatttgatattggtgatgagtaattttttgattaaatattggatgctgaatggttgtagTTATAATCCTCTGGAGAGGAGAGAGGTTAGCAAAGGTGGAAGAGAAACGAGCAAGAAATCTGCAAACTCGCAAGCCTCAACGAAGGGTTCTACTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -tcttgtg
- - - - - - acctttg
- - - - - - - - - - - - tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgct