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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGAGAGATACCAGTTATTGCAGCTGGAGGAATTGTGGATGCTCGGGGTTATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaatattacttttacattaatcatatttgaggaaattgttctcatattgttgcagtaatttcttagcatatgcagtttttgtgttcaacttaag...

Basic information

species Glycine max
transcript GLYMA08G18990.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18990.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G64250.2 (Arabidopsis thaliana), 5'ss of exon 3
ACCGAGAGATACCAGTTATTGCAGCTGGAGGAATTGTGGATGCTCGGGGTTATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaatattacttttacattaatcatatttgaggaaattgttctcatattgttgcagtaa-tttcttagcatatgcagtttttgtgttcaacttaag
| || || || || |||||||| |||||||||||||||||||  || ||||||||||| ||| |  ||||||| |||||||| |||||||||||||| |||| |        | |||||     |    |  |  ||     | ||  | | ||||||   | | ||| |||| || | |  ||| |  |           
AACGCGATATTCCCGTTATTGCTGCTGGAGGAATTGTGGATGGACGCGGTTATGTTGCAGCTTTGTCACTTGGGGCTCAAGGGGTCTGTCTAGGCACAAGgtgt--gtgctcttcttttgttccacatgttctcaagtttgatattagctttttgttgggctgagttttttagaatcttcgttttcttag-----------

upper sequence: GLYMA08G18990.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0017g01240.t01 (Vitis vinifera), 5'ss of exon 4
ACCGAGAGATACCAGTTATTGCAGCTGGAGGAATTGTGGATGCTCGGGGTTATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgt-------tttgaaatattacttttacattaatcatatttgaggaaattgttctcatattgttgcagtaatttcttagcatatgcagtttttgtgttcaacttaag
| ||||| ||||| || ||||| ||||| || ||||| ||||  || || |||||||||||| | || |||||||| |||||| |||| |||||||| ||||       |||| || | ||  |||  | |  | | ||        |   |    |     || || |  ||  | |   ||||  ||||   |   ||||     
ATCGAGACATACCGGTAATTGCTGCTGGGGGTATTGTTGATGAGCGTGGATATGTTGCTGCTTTGGCTCTTGGTGCCCAAGGCATCTGCCTAGGCACAAGgtatatatatttgtaagactatctttgaaatgctaaaatagagaacgaaaataggaaatccatttcattttttattca--ttatggtgtttagattaccaac-----
















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|254333238|gb|GR850488.1|GR850488
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|24136645|gb|BU927155.1|BU927155
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGGCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCAT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCAT
EST: gi|254336981|gb|GR843160.1|GR843160
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAA-GGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|6847210|gb|AW349500.1|AW349500
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|120533082|gb|EH261215.1|EH261215
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|120491988|gb|EH220155.1|EH220155
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|120491921|gb|EH220088.1|EH220088
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|254333239|gb|GR850489.1|GR850489
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|254336982|gb|GR843161.1|GR843161
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
EST: gi|151409674|gb|EV279482.1|EV279482
EST:     TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAG                         GTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT
genomic: TATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaat ... ttgtttgcagGTTTTTGGCTACTGAGGAAAGCAATGCTCATCCTACATACAAAAGGAAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGAGAGATACCAGTTATTGCAGCTGGAGGAATTGTGGATGCTCGGGGTTATGTTGCTGCTCTAGCACTTGGTGCTCAAGGCGTCTGTCTAGGCACTAGgttttgaaatattacttttacattaatcatatttgaggaaattgttctcatattgttgcagtaatttcttagcatatgcagtttttgtgttcaacttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT