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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accttgggttcctaatccaggacaaaatggttacaggaacaaggttgtttttgcattgacttttcattatgaataatgttctatacatttaacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTATGTTTATTGAGGCTAGTGCAAAAGCCGGCTTTAATATAAAG

Basic information

species Glycine max
transcript GLYMA05G05860.1
intron # 4
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|192325163|gb|FK017534.1|FK017534
EST:     GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAG                         GCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
genomic: GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgtaatggcta ... aacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
EST: gi|13252783|gb|BG363686.1|BG363686
EST:     GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAG                         GCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
genomic: GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgtaatggcta ... aacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
EST: gi|192321239|gb|FK014329.1|FK014329
EST:     GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAG                         GCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
genomic: GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgtaatggcta ... aacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
EST: gi|31459979|gb|CD402007.1|CD402007
EST:     GATGTTATTGTGGTTCTTGTTGGGAACCAAACTGATCTTGTGGATAAAAG                         GCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
genomic: GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgtaatggcta ... aacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
EST: gi|192322379|gb|FK014620.1|FK014620
EST:     GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAG                         GCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
genomic: GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgtaatggcta ... aacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTAT
EST: gi|192321240|gb|FK014330.1|FK014330
EST:     GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAG                         -CAAGTCTCTACAGAGGAAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTA
genomic: GATGTTATTGTGGTTCTTGTTGGGAACAAAACTGATCTTGTGGATAAAAGgtaatggcta ... aacacttcagGCAAGTCTCTACAGAGGAA-GGGGAAGCAAAGTCCCGAGAGCTAAACGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgcattgacttttcattatgaataatgttctatacatttaacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTATGTTTATTGAGGCTAGTGCAAAAGCCGGCTTTAATATAAAG
                                         atttaac  putative branch site (score: 3)
                    attatgaataatgttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accttgggttcctaatccaggacaaaatggttacaggaacaaggttgtttttgcattgacttttcattatgaataatgttctatacatttaacacttcagGCAAGTCTCTACAGAGGAAGGGGAAGCAAAGTCCCGAGAGCTAAACGTTATGTTTATTGAGGCTAGTGCAAAAGCCGGCTTTAATATAAAG

- - - -gttccta
- - - - - - - - ccaggac
- - - - - - - - - - - - - - - - - - - - - ggttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg