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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatatacatgcactgtgttcctttttatgatccttataaacatcctagctaaaaatcataaatgatggactactatattgtaattctctctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATGAAGCGGCAAATAGGGCTGCAATTTGTTCGTCCGGCAGGATCATGATGAT

Basic information

species Glycine max
transcript GLYMA13G30060.3
intron # 10
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|15199982|gb|BI424109.1|BI424109
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
EST: gi|31471662|gb|CD413690.1|CD413690
EST:     CTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: CTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
EST: gi|33390223|gb|CA853430.1|CA853430
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
EST: gi|21888427|gb|BQ741640.1|BQ741640
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
EST: gi|193410696|gb|FK375885.1|FK375885
EST:     GCCTGCCAAATGGTCGTCCATTTCCNCCTTTATTTAACTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
EST: gi|26057508|gb|CA800422.1|CA800422
EST:     CCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: CCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
EST: gi|14991336|gb|BI317009.1|BI317009
EST:     GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAA                         TTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG
genomic: GCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtcctt ... ctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagctaaaaatcataaatgatggactactatattgtaattctctctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATGAAGCGGCAAATAGGGCTGCAATTTGTTCGTCCGGCAGGATCATGATGAT
  agctaaa  putative branch site (score: 3)
                                       ttctctctgtttcc  putative PPT
     taaaaatcataaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatatacatgcactgtgttcctttttatgatccttataaacatcctagctaaaaatcataaatgatggactactatattgtaattctctctgtttccagTTATCCGAAGCTTCTCCAGAGCTTGTGAACAAAGTGATACCTGACCACATGAAGCGGCAAATAGGGCTGCAATTTGTTCGTCCGGCAGGATCATGATGAT

- - - -catgcac
- - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgg