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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctgagtcgtttaatggtttatgcttgttgttttgacctgatctgtgttcggtcaaagttgctcgttcatccttgaactgatattgtttcactgtatgacaatttcagtagtgtgtgtgttttggttgactttggatttggattaatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA

Basic information

species Glycine max
transcript GLYMA19G40930.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G40930.4 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 2
gtattctgagtcgtttaatggtttatgcttgttgttttgacctgatctgtgttcggtcaaagttgctcgttcatccttgaactgatattgtttcactgtatgacaatttcagtagtgtgtgtgttttggttgactttggatttggattaatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                                         ||          |   |||| ||| |    |  |  |  | | |  |  ||||  |    ||||  | ||   | || |||   ||    |  |    ||||| ||||||||    |||||||||||||||||||| ||||| ||||| |||||  ||||||| ||| | |||| ||| |||||| |  || ||
-----------------------------------------------------gacacatgacaaaatatctttcctcgaaatttggtcatcgctttttgtacctctttctttt-catgtgactatttcataacattgctatt----tgttcctacagGTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA

upper sequence: GLYMA19G40930.4 (Glycine max), 3'ss of exon 3
lower sequence: AT3G62120.2 (Arabidopsis thaliana), 3'ss of exon 2
gtattctgagtcgtttaatggtttatgcttgttgttttgacctgatctgtgttcggtcaaagttgctcgttcatccttgaactgat-attgtttcactgtatgacaatttcagtagtgtgtgtgttttggttgactttggatttggattaatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                                                | | ||| ||   |  |  ||| | ||||||     |      |||  ||     |   ||| |   |||| |  | |||   |||  |  |     | |||| ||    || |||||||||||||| ||||| || || || ||||||||  |||| ||||||||||| || |||||||| ||||||
----------------------------------------------------------------gtttgtttatatgttcaacgatgagtgtttc----cacattcttttttgtcccaagctggttata--tgacatctgcttttctttatgtctgtctagGTTTGTAAACA-AGATATGATTGAGTACTACGATATCTCTGGATGTTATATTCTACGGCCATGGTCAATGGCCATTTGGGAGATTATGCAA

upper sequence: GLYMA19G40930.4 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 3
gtattctgagtcgtttaatggtttatgcttgttgttttgacctgatctgtgttcggtcaaagttgctcgttcatccttgaactgatattgtttcactgtatgacaatttcagtagtgtgtgtgttttggttgactttggatttggattaatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                          ||||   |||||| |  ||  ||||  | | | || |   | ||||| ||  | ||||  |  |||   |   | ||    | |  | |  |||||| ||  | |||  || ||        || ||||  ||||||||||||||||||||||| || || || || ||||||||||| ||| | |||||| | |||||||  ||||||
------------------------------------------tgattcatgttcgatataa--tgct--tccttgctagctatcatatt-ttagaatgtacaagtattgttgccct-tgaccatctaagctttctttggttt--gtttagGTTTGC--------GTCAATGGTGAAATGATTGAGTACTATGATATATCAGGCTGTTACATTCTGAGGCCATGGACTATGGCAGTCTGGGAGACGATGCAA

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|209707571|gb|BW680941.1|BW680941
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|208308087|gb|GE105483.1|GE105483
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|7591393|gb|AW707127.1|AW707127
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|209700498|gb|BW664460.1|BW664460
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|193444216|gb|FK409738.1|FK409738
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|213604934|gb|DB956323.1|DB956323
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|193310687|gb|FK274611.1|FK274611
EST:     AGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: AGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
EST: gi|208266921|gb|GE062316.1|GE062316
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattctgag ... aatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttcagtagtgtgtgtgttttggttgactttggatttggattaatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                         gattaat  putative branch site (score: 3)
                                    atttggattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctgagtcgtttaatggtttatgcttgttgttttgacctgatctgtgttcggtcaaagttgctcgttcatccttgaactgatattgtttcactgtatgacaatttcagtagtgtgtgtgttttggttgactttggatttggattaatttggcagGTGGTTGTTAATGCGGAAATGATTGAGTACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA