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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcattcccctaagccaaactaacaaaattagattatctttcaattttatgctttagattgatataccatttttctttcttctccacttgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAAGCATTTTACAAGTTGCCAAGATGGAAGCAAGACATGCTGAAAAAGAAAT

Basic information

species Glycine max
transcript GLYMA10G21350.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 22
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 24
cttgcattcccctaagccaaactaacaaaattagattatctttcaattttatgctttagattgatataccatttttctttcttctccacttgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAAGCATTTTACAAGTTGCCAAGATGGAAGCAAGACATGCTGAAAAAGAAAT
      |    | ||    | |  |     ||   || ||||||   || ||  || ||  | |  |  || | |  | |       ||   |   |||||| || ||||| ||||  |||||||| ||||||||||| ||||  |||||| |||| ||||| |||||  ||||||| |||||| | ||||| |||||||
-----gtgaatcaaaattgagccgattttgttctttt-tctttcgtcttaat--ttgagcataagttgtcagtatcttattcctcaaaccaatttatcagGCTTACCTGTCTGAGGTAGAGTTCAAGACTGTATTTGGGATGGAGAAAGAATCATTCTACAAATTGCCTGGATGGAAACAAGACTTACTGAAGAAGAAAT

upper sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 22
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 21
-cttgcattcccctaagccaaactaacaaaattagattatctttcaattttatgctttagattgatataccatttttctttcttctccacttgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAAGCATTTTACAAGTTGCCAAGATGGAAGCAAGACATGCTGAAAAAGAAAT
  | |     |  |||     ||||      ||  |  ||   |||  ||| |  ||   |||   | |  ||||  ||||      || | |     ||||||||||||||||| || |||||| | || ||| | || ||| | ||||| ||||| || || ||||| | ||||||||||||||||   || |||||| 
gttggttcaactttaaatatgactatttcgttttaa--attcctcatgtttttatttgcaatttcaaaaaaatttccctttg-----cattcg-----cagGCCTATCTGTCAGATGAGGAGTTCCAGACCGTACTGGGGATGACCAAAGACGCATTCTATAAATTGCCCAAATGGAAGCAAGACATGACAAAGAAGAAAG
















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|18734486|gb|BM528211.1|BM528211
EST:     AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAG                         GCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
genomic: AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAGgttagtcttg ... tgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
EST: gi|193526853|gb|FK487165.1|FK487165
EST:     AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAG                         GCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
genomic: AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAGgttagtcttg ... tgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
EST: gi|192326285|gb|FK017632.1|FK017632
EST:     AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAG                         GCCTACCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
genomic: AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAGgttagtcttg ... tgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
EST: gi|6667331|gb|AW278782.1|AW278782
EST:     AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAG                         GCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
genomic: AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAGgttagtcttg ... tgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
EST: gi|208167861|gb|GD959997.1|GD959997
EST:     AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAG                         GCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA
genomic: AGACTAAATCTGGTCATAATGTGCCTGGAGTTGATCTTAAACGGAGAGAGgttagtcttg ... tgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatgctttagattgatataccatttttctttcttctccacttgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAAGCATTTTACAAGTTGCCAAGATGGAAGCAAGACATGCTGAAAAAGAAAT
             gattgat  putative branch site (score: 4)
                     taccatttttctttct  CT-rich tract
         tttagattgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcattcccctaagccaaactaacaaaattagattatctttcaattttatgctttagattgatataccatttttctttcttctccacttgtcggtcagGCCTATCTGTCAGAGGATGAGTTCAACACTGTATTTGGAATGGCAAAAGAAGCATTTTACAAGTTGCCAAGATGGAAGCAAGACATGCTGAAAAAGAAAT

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