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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacagaggatcaatcgaagcatcacttaattttcattacatccattaatcttgcctacgatttttttttattttttttttttgctttgccctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAATAACTTCTTTTTTTTACGAGATTCTATAGCAACGTGCATAGAAGTCAAG

Basic information

species Glycine max
transcript GLYMA20G39220.1
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|19937550|gb|BQ081335.1|BQ081335
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
EST: gi|22933661|gb|BU550800.1|BU550800
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
EST: gi|22928310|gb|BU545449.1|BU545449
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
EST: gi|21887280|gb|BQ740493.1|BQ740493
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
EST: gi|16346863|gb|BI972458.1|BI972458
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
EST: gi|17154048|gb|BM143981.1|BM143981
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
EST: gi|16346817|gb|BI972412.1|BI972412
EST:     TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAG                         AAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA
genomic: TGCTCGATTTGGCCGTTCAACACATTAAAGGTCTTCAAACTCAGGTTCAGgtctgtataa ... cctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatcttgcctacgatttttttttattttttttttttgctttgccctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAATAACTTCTTTTTTTTACGAGATTCTATAGCAACGTGCATAGAAGTCAAG
 cattaat  putative branch site (score: 3)
                tttttttttatttttt  putative PPT
           tacgatttttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacagaggatcaatcgaagcatcacttaattttcattacatccattaatcttgcctacgatttttttttattttttttttttgctttgccctctttcagAAGCTTCACAAAGAAATGGAGAATTGCACTTGCGGATGCAAACAAAGCAAATAACTTCTTTTTTTTACGAGATTCTATAGCAACGTGCATAGAAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - acatcca