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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaacggttttatggtttgcttaggttttattttgaattgtgttgtgaggccctaactgtttacccacacgtctatctttaatttataaatatttatttgtatgattttcttagatgtcttttttgtttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGCAGACTATGCAAAGAATGAAATTCAACGTCTTGAGCGCATGCTTGAGAAG

Basic information

species Glycine max
transcript GLYMA19G41690.1
intron # 9
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|208165786|gb|GD959490.1|GD959490
EST:     TTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
EST: gi|209699182|gb|BW664359.1|BW664359
EST:     TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTCCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
EST: gi|10255939|gb|BE823705.1|BE823705
EST:     TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGTTTCTTCTGCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
EST: gi|21600775|gb|BQ611106.1|BQ611106
EST:     TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
EST: gi|58024257|gb|CX710998.1|CX710998
EST:     TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
EST: gi|209720793|gb|BW657767.1|BW657767
EST:     TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
EST: gi|15337327|gb|BI497983.1|BI497983
EST:     TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAG                         ACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC
genomic: TATTCCCGGCTTGAGGAGGAAGTTAAGAAGCTTAAAGGTTCTTCTGCCAGgtttgaacgg ... tttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttataaatatttatttgtatgattttcttagatgtcttttttgtttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGCAGACTATGCAAAGAATGAAATTCAACGTCTTGAGCGCATGCTTGAGAAG
 ctttaat  putative branch site (score: 4)
                                  tgtcttttttgttt  putative PPT
     taaatatttatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaacggttttatggtttgcttaggttttattttgaattgtgttgtgaggccctaactgtttacccacacgtctatctttaatttataaatatttatttgtatgattttcttagatgtcttttttgtttgtaccagACATGGCGACCTTTACTTAAAACTTGCTAAGAAGGGTATGGAAAAGGGTGCAGACTATGCAAAGAATGAAATTCAACGTCTTGAGCGCATGCTTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA