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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttaagataatgtttttatatgtgtagagtcctctcttgcctcctctttctttttggtcagaatggaaaggttaatagtgctatgtgtgtggattatttctatctgctatttgtgctaaccttccagtgattaatatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTGATGGCTAAGGCCAATGTTGTTATCAACCTTATTG

Basic information

species Glycine max
transcript GLYMA13G18950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 3'ss of exon 4
gtagttaagataatgtttttatatgtgtagagtcctctcttgcctcctctttctttttggtcagaatggaaaggttaatagtgctatgtgtgtggattatttctatctgctatttgtgctaaccttccagtgattaatatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTGATGGCTAAGGCCAATGTTGTTATCAACCTTATTG
                |   |||  ||  || |  |   |||  ||   |||    || ||  || | |   ||  || |||  | ||  ||     ||||||  | |   ||||      || ||    ||| | |||    ||||| ||||| ||||||||||||||||| ||||||| |||  | || || || ||||| || || || |||||| |||| |||||||
---------------gtagaataaatggtgatttattcattgattcaaattttccatttgtgtgacttggtggg--aacagtagtttggctgg----tatttcctttta--attta----gactttt---tgactgatactatcagATAGTACCAATGAAATACAATCCAAGAGATGAAAATTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG
















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|209703775|gb|BW670711.1|BW670711
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAATACAATCCAAGGGAT
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGAT
EST: gi|151400304|gb|EV270118.1|EV270118
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|298181570|gb|HO025745.1|HO025745
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|192301726|gb|FG997640.1|FG997640
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|298190384|gb|HO032505.1|HO032505
EST:     GCTCTGGAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|151398563|gb|EV268434.1|EV268434
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|298192730|gb|HO033164.1|HO033164
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|151403355|gb|EV273165.1|EV273165
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|209718615|gb|BW662707.1|BW662707
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|254347887|gb|GR854136.1|GR854136
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|213595497|gb|DB966551.1|DB966551
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|192312569|gb|FK005027.1|FK005027
EST:     CTCTGA-GAATAATCCCCGTCATCTCAAATTGGTGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: CTCTGAAGA-TAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|213591304|gb|DB959874.1|DB959874
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|151397287|gb|EV267160.1|EV267160
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|298184881|gb|HO030094.1|HO030094
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|209707137|gb|BW656754.1|BW656754
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAAT
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAAT
EST: gi|12774559|gb|BG239486.1|BG239486
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAAGCTGT
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAA-GCTGT
EST: gi|14258415|gb|BG881323.1|BG881323
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|209709595|gb|BW661922.1|BW661922
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|209714364|gb|BW677064.1|BW677064
EST:     GCTCTGAAGATAATCCCCGACATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCAATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|298174324|gb|HO017660.1|HO017660
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|192312568|gb|FK005026.1|FK005026
EST:     CTCTGA-GAATAATCCCCGTCATCTCAAATTGGTGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: CTCTGAAGA-TAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
EST: gi|192300056|gb|FG991860.1|FG991860
EST:     GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAG                         ATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG
genomic: GCTCTGAAGATAATCCCCGTCATCTCAAATTGATGGGGGATTTGGGACAGgtagttaaga ... atatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggattatttctatctgctatttgtgctaaccttccagtgattaatatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTGATGGCTAAGGCCAATGTTGTTATCAACCTTATTG
     ttatttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttaagataatgtttttatatgtgtagagtcctctcttgcctcctctttctttttggtcagaatggaaaggttaatagtgctatgtgtgtggattatttctatctgctatttgtgctaaccttccagtgattaatatgcccagATTGTACCCATGAAATACAATCCAAGGGATGAAAGTTCAGTAAAAGCTGTGATGGCTAAGGCCAATGTTGTTATCAACCTTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG