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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatgcctaggaaagatgcaaagtccattgcaaacgtttaagcaaacatgcactaagtgaataagtttgactaacctaagtttctaatggtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCGGACTCAACGGGATCTTTTGTGATATATGCTCCTGTAGATATTGTGGCAA

Basic information

species Glycine max
transcript GLYMA12G32050.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G32050.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 10
-----tctatgcctaggaaagatgcaaagtccattgcaaacgtttaagcaaacatgcactaagtgaataagtttgactaacctaagtttctaatggtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCGGACTCAACGGGATCTTTTGTGATATATGCTCCTGTAGATATTGTGGCAA
| || | || | | | || ||| ||| || || || | || | || ||||| || || | | ||||||| ||||||||||| ||||||||||||||||| ||||| || || | || ||||| | ||||| ||||| ||||||||||| ||| |||| || |
gtaggttaatatttctataattttctagttc--ttgttcttattttagtgcttgtgtcct---tcaaccaacatgcttaacc---attgtgaacatttc---tagAGTGCAAATTCAAGCCAGAGCAACATGTTGATATTGCAAGAAAGCTGTACTGATTCAACAGCCTCTTTCGTGATTTATGCTCCTGTCGATGTTGTTGCCA
















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|208193920|gb|GD989793.1|GD989793
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
EST: gi|6227856|gb|AW156455.1|AW156455
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
EST: gi|208307838|gb|GE104982.1|GE104982
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
EST: gi|298166235|gb|HO009206.1|HO009206
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
EST: gi|193386002|gb|FK352372.1|FK352372
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTAACAAGAGAGTTG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTA-CAAGAGAGTTG
EST: gi|120532754|gb|EH260887.1|EH260887
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
EST: gi|193620940|gb|FK569994.1|FK569994
EST:     CACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: CACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
EST: gi|120532424|gb|EH260557.1|EH260557
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACANAGAGAGTTGCGC
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACA-AGAGAGTTGCGC
EST: gi|207755393|gb|GD729428.1|GD729428
EST:     TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAAT                         AGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG
genomic: TTGCCAATGGCCGAGACACTGGAAATTGTGTCTCTCTACTTCGGGTGAATgtaagttgac ... gtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatgcactaagtgaataagtttgactaacctaagtttctaatggtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCGGACTCAACGGGATCTTTTGTGATATATGCTCCTGTAGATATTGTGGCAA
               aataagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatgcctaggaaagatgcaaagtccattgcaaacgtttaagcaaacatgcactaagtgaataagtttgactaacctaagtttctaatggtgcatgcagAGTGCGAATTCAAGCCAAAGCAACATGTTGATATTACAAGAGAGTTGCGCGGACTCAACGGGATCTTTTGTGATATATGCTCCTGTAGATATTGTGGCAA

-ctatgcc
- - - - - - - -gatgcaa
- - - - - - - - - - - - -ccattgc
- - - - - - - - - - - - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaacc