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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAATGATGGAGGATGACATGGAGACCGGTACTTTGGGGGCTTACCAGGACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgtttttcgttcccaaaccccacctcattcataactcacttcttcattatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctcatgcttgccttcttccatatttctgcag

Basic information

species Glycine max
transcript GLYMA08G24120.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24120.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 2
TATAATGATGGAGGATGACATGGAGACCGGTACTTTGGGGGCTTACCAGGACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgtttttcgttcccaaaccccacctcattcataactcacttcttcattatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctcatgcttgccttcttccatatttctgcag
| |||  ||||| || ||  ||||||  ||| |||||||| ||||||| || |||| ||| |  |||||||||||||| | |||| ||||||||||| ||||  |      ||      | |   | |  |   ||||    ||| ||| | ||  ||| | |  | ||||   ||    | |   |   |      |||  |||||                                   
TGTAACTATGGATGACGATGTGGAGAGTGGTGCTTTGGGGCCTTACCAAGATAAGCCAAGGATTTTCCCCAACATGCGGAGTAAATCTTACACCCCATTGgtaaggacactgt------atctgtctttgtagttaacatgtttcctcagt-tacttatgtttgga-atattcttaccctttttggttcttggggtaatac-tatattg---------------------------------
















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|213618250|gb|DB973020.1|DB973020
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
EST: gi|213598957|gb|DB971957.1|DB971957
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTA
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTA
EST: gi|308098348|gb|HO760089.1|HO760089
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
EST: gi|209725685|gb|BW663176.1|BW663176
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
EST: gi|120529403|gb|EH257537.1|EH257537
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
EST: gi|207716770|gb|GD699784.1|GD699784
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCT
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCT
EST: gi|213588572|gb|DB957636.1|DB957636
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
EST: gi|213588412|gb|DB959732.1|DB959732
EST:     ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTG                         ATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG
genomic: ACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgttttt ... atttctgcagATATTTCGTATTCTATTGGGTATCAATGTTCGTGTCCTCTTCATTCTTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAATGATGGAGGATGACATGGAGACCGGTACTTTGGGGGCTTACCAGGACAAGCTAAGAACCTTCCCCAACATGCGCACTAAACCTTACACCCCACTGgttcgtttttcgttcccaaaccccacctcattcataactcacttcttcattatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatctcatgcttgccttcttccatatttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC