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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattacgtccgcgtacttaaaaattttaatctaaattttatttatttaatattattttttgttggagggaaaattgagatgttattgttatgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTATGTGTCCGAGGAAGTGTGGCGGCGGCGGCGGCGACGGTAGAGGAACGAC

Basic information

species Glycine max
transcript GLYMA12G09010.1
intron # 2
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|209728196|gb|BW651631.1|BW651631
EST:     CAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|51338436|gb|CO982302.1|CO982302
EST:     CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|120530327|gb|EH258460.1|EH258460
EST:     CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|16349232|gb|BI974827.1|BI974827
EST:     CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|19452731|gb|BM954141.1|BM954141
EST:     CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|21994610|gb|BQ786138.1|BQ786138
EST:     CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|254329566|gb|GR839119.1|GR839119
EST:     CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CAACGACCCTTCCCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
EST: gi|9903352|gb|BE612320.1|BE612320
EST:     CCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAA                         GTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA
genomic: CCACTTCGACCTTCATTATTCTCAGTTCAGCTTAGAAAgtaagcgtct ... atgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatattattttttgttggagggaaaattgagatgttattgttatgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTATGTGTCCGAGGAAGTGTGGCGGCGGCGGCGGCGACGGTAGAGGAACGAC
 atttaat  putative branch site (score: 4)
     tattattttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattacgtccgcgtacttaaaaattttaatctaaattttatttatttaatattattttttgttggagggaaaattgagatgttattgttatgtgtgcagGTTTGGATAGGGAGGAGAAGCTGAGGGATATTGGATCTAGAAACTTCTTTATGTGTCCGAGGAAGTGTGGCGGCGGCGGCGGCGACGGTAGAGGAACGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggaggg