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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG

Basic information

species Glycine max
transcript GLYMA13G21310.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G21310.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 9
gtaaagtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG
      |||| |  || |||| | | | | ||  |       | |     ||       |  |   |   | || ||| |    |    | | ||  | || |   ||||||| ||||| ||||||||||| ||||||||||| || |||||  | || || || || |||||| | || || || ||||| || |||| ||
-----ttata-atcatttatgttatgtgattttcggcgttctttgccccttttttcctgttttgtcatttatttcactgtttgtgggattgtcat--ttatttgtcagGTTGCAAGTGCAACAGCAACATTCGTGATGATGTTCTCCTCATCCCTATCCGTAGTGGAGTTCTACTTCCTGAACAGATTCCCAATCCCTTTTG

upper sequence: GLYMA13G21310.2 (Glycine max), 3'ss of exon 9
lower sequence: AT2G36630.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaagtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG
            ||| | |  |  ||| |   |     |   | || |||       ||||||  |  |   |     ||  |    ||| | |   | |      |||||||||| || ||||| || ||||||||||||||||| || || || || || || || ||||| || |||||||| ||||| || || || |
------------gtaaacacaccatcttatcagtatatatgattgtaaaacc-----cataatcattcatcttgtgtctttcatttttatctaacggttaaaacacagGTTGCTAGCGCAACAGCTACCTTTGTGATGATGTTTTCTTCGTCCTTATCCGTAGTCGAGTTCTATCTCCTCAAGAGATTCCCAATACCATACG

upper sequence: GLYMA13G21310.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g04230.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------gtaaa-gtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaactta----actttaaaagaatatttgatcataatctt--gtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG
                                                  |||   | |  |||  ||  || | |   |||     |   |||| ||   ||   |   |      | | |||||    | | |||| ||||   | |   |   |||    ||||||| || || |||||||| |||||||||||||| |||||||| || || || || || |||||||| ||||||||||| |||||||| ||||
gtatgtgactttgatgggtatctctaattgcaatggcctgtccaacctttgtacctgaacttagattacctgttataagaatcagaatt-tactactttctttgtcattctccgctaaaacacttacgatattataaaggaatgaataactgttggctttcacagGTTGCAAGCGCGACAGCAACTTTTGTGATGATGTTCTCATCATCCTTATCTGTTGTGGAGTTCTACCTCCTCAAGAGGTTTCCCATTCCATATG

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|193386378|gb|FK350382.1|FK350382
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|208108275|gb|GD901625.1|GD901625
EST:     GTGGATTTGTTTTGGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTCTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193364959|gb|FK333216.1|FK333216
EST:     TGGGTTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: TGGG-TTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193689584|gb|FK628827.1|FK628827
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|207707045|gb|GD689189.1|GD689189
EST:     AGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: AGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193495500|gb|FK461496.1|FK461496
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACGGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193445565|gb|FK412656.1|FK412656
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|208256299|gb|GE057058.1|GE057058
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|192317082|gb|FK007849.1|FK007849
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|208295832|gb|GE092207.1|GE092207
EST:     TTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: TTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193337052|gb|FK302432.1|FK302432
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193556361|gb|FK513600.1|FK513600
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193494884|gb|FK460618.1|FK460618
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193462922|gb|FK427365.1|FK427365
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|208112947|gb|GD910586.1|GD910586
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCACCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193617270|gb|FK567488.1|FK567488
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|192317081|gb|FK007848.1|FK007848
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|14126025|gb|BG790463.1|BG790463
EST:     GTGGGTTTGTTTTAAGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|207766033|gb|GD735534.1|GD735534
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|193481968|gb|FK444399.1|FK444399
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|208245155|gb|GE037013.1|GE037013
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
EST: gi|207765830|gb|GD735471.1|GD735471
EST:     GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAG                         GTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA
genomic: GTGGGTTTGTTTTAGGACCTCTTCTTCTAGAGATTGGTGTCATTCCTCAGgtaaagtata ... aatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG
     ataattctagaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtatatagtatatatgctctctcaattgagctaacactagttaaattaggagcataattctagaaacttaactttaaaagaatatttgatcataatcttgtagGTTGCTAGTGCTACAGCAACATTTGTGATGATGTTTTCATCATCTTTGTCAGTGGTTGAATTCTACCTTCTCAAGAGGTTCCCCATTCCTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG