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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagtgcaaatcgaaggggagatcagagtaatttttcctgctttttttggctacactttaattctttatctttgcgctcatgatatacttgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAA

Basic information

species Glycine max
transcript GLYMA09G39150.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 7
attagtgcaaatcgaaggggagatcagagtaatttttcctgctttttttggctacactttaattctttatctttgcgctcatgatatacttgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAA
    |||   ||    |    |  ||   ||   ||  |||||| ||| |  ||   | | |      |  | |   |||  | | |  |       ||||||||||||||  | ||| ||||||| || |||||||||||||| || || || | ||| || ||||| || ||||||||||||||||| ||||| ||||
----gtgtgtatttctgtcatggccattttacaattcactgcttgttt-gcatatgttgttaccagacaa-tataatctcccgcttttttatggctatagCTTCCAGATGGAGACCTCCGGGAGAAGATTGAGAAACTTGCTTCTTCTCTAAAGTTTCCTTTGAAGAAGCTGTTTGTTGTCGATGGATCTACAAGGTCAA

upper sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 7
---attagtgcaaatcgaaggggagatcagagtaatttttcctgctttttttggctacactttaattctttatctttgcgctcatgatatacttgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAA
   | || |   | ||          | |     |  |    |   ||| |||  ||   |   | | ||  | |    |    || |  |    | || |||||||| |||||| | |||||||| | ||| |||||||||||||| ||||| || | ||| ||||||||  | || ||||| |||||||| ||||| ||||
gtgagtattttcattctttcattctgtaaagaagaaatgcattcagtttcttgtttagtgtaacagttttcttttccatgtctctgctgca----acaagtagCTTCCTGATGGTGAGCTCAGGGAAAGAATTGAGAAACTTGCTTCGTCCCTTAAGTTTCCCTTAAAGAAGTTGTTCGTTGTTGATGGATCTACAAGGTCAA
















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|207843659|gb|GD813872.1|GD813872
EST:     TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCA                         CTTCCAGATGGTCAACTCAGGGAGAAAA
genomic: TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCAgtaagaattt ... tgataactagCTTCCAGATGGTCAACTCAGGGAGAAAA
EST: gi|151398881|gb|EV268752.1|EV268752
EST:     GACCCTTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCA                         CTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
genomic: GACCC-TTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCAgtaagaattt ... tgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
EST: gi|5175463|gb|AI759796.1|AI759796
EST:     TGA-CCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCA                         CTT-CAGAATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCT
genomic: TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCAgtaagaattt ... tgataactagCTTCCAG-ATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCT
EST: gi|17519798|gb|BM188840.1|BM188840
EST:     TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCA                         CTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
genomic: TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCAgtaagaattt ... tgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
EST: gi|308099210|gb|HO761388.1|HO761388
EST:     ACTAATAGCTCCACTCTTCAATAAGTTCACTCCA                         CTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
genomic: ACTAATAGCTCCACTCTTCAATAAGTTCACTCCAgtaagaattt ... tgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
EST: gi|5175455|gb|AI759788.1|AI759788
EST:     TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCA                         CTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC
genomic: TGACCCTTTATCCAGTACTAATAGCTCCACTCTTCAATAAGTTCACTCCAgtaagaattt ... tgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggctacactttaattctttatctttgcgctcatgatatacttgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAA
            tttaattctttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagtgcaaatcgaaggggagatcagagtaatttttcctgctttttttggctacactttaattctttatctttgcgctcatgatatacttgataactagCTTCCAGATGGTCAACTCAGGGAGAAAATCGAGAAACTTGCTTCCTCCCTCAACTATCCGTTAAAGAAACTATTTGTTGTCGATGGATCCACAAGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
-ttagtgc
- - - - - - -gaagggg
- - - - - - - - - - - - - - - - - - tcctgct
- - - - - - - - - - - - - - - - - - - - - - - - tggctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatga