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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagaataactgacttgtatatgggtagtgttatattgtttgtggttcccttttactcagataatttgtgttcttatcaaattgctggctggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGATGAGGATGAAGGACTAGAAGAGGAAGATAATGATGAACATGGAGATACCT

Basic information

species Glycine max
transcript GLYMA13G42250.1
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|151407239|gb|EV277054.1|EV277054
EST:     CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCG                         CGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
genomic: CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCGgtaaacaata ... ggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
EST: gi|16280374|gb|BI943929.1|BI943929
EST:     TTCGGTTTC-AACAACAGGTGGCAGCAAATCTAAGTCTAACTCTAAAGCG                         CGGGCTTCCGAAACCAAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
genomic: TTCGGTTTCAAACAACA-GTGGCAGCAAATCTAAGTCTAACTCTAAAGCGgtaaacaata ... ggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
EST: gi|151396879|gb|EV266752.1|EV266752
EST:     CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCG                         CGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
genomic: CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCGgtaaacaata ... ggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
EST: gi|192327672|gb|FK020677.1|FK020677
EST:     CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCG                         CGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
genomic: CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCGgtaaacaata ... ggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
EST: gi|8403706|gb|BE059402.1|BE059402
EST:     CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCG                         CGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
genomic: CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCGgtaaacaata ... ggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
EST: gi|192327673|gb|FK020678.1|FK020678
EST:     CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCG                         CGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT
genomic: CTTCGGTTTCAAACAACAGTGGCAGCAAATCTAAGTCTAACTCTAAAGCGgtaaacaata ... ggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcccttttactcagataatttgtgttcttatcaaattgctggctggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGATGAGGATGAAGGACTAGAAGAGGAAGATAATGATGAACATGGAGATACCT
                            ttatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagaataactgacttgtatatgggtagtgttatattgtttgtggttcccttttactcagataatttgtgttcttatcaaattgctggctggtggagcagCGGGCTTCCGAAACCCAGGGCAGACAATCAAAGCCATTACAACCAAAAGATGAGGATGAAGGACTAGAAGAGGAAGATAATGATGAACATGGAGATACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- -gaataac
- - - - - tgacttg
- - - - - - - - - - - -ggtagtg
- - - - - - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctggc