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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC

Basic information

species Glycine max
transcript GLYMA03G42370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
--------------gtgaatggctaagatgcaccttctatttattttatatttttcgt-tgtttccatgacatgatttcatctgactaaaat----ttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
              |||||   || | | | || |   | || || |  | ||   ||   | |   ||||| |  |   |||||  ||||     ||||  |  | |||||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||
gtatgtgcaacattgtgaa-aactcacaagaacttatcaatt-ttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
gtgaatggctaaga-tgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
      ||||  || | |        || ||    | ||||||  ||    ||||  |  |||||     |  ||||| |  | |  | |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||| |||||||| |
------ggctgtgaatccgtaaaaggttcatccagtttttttc-ctgcacacatgttaatatttc--tgaaacaaaatattctat--tgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
----gtgaatggctaaga-tgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
     |  | ||||  || | |        || ||    | ||||||  ||    ||||  |  |||||     |  ||||| |  | |  | |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||| |||||||| |
gtatatctagggctgtgaatccgtaaaaggttcatccagtttttttc-ctgcacacatgttaatatttc--tgaaacaaaatattctat--tgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
----gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
     |  ||||||  ||  |      |||| ||   |   ||||| | ||     ||       |   |||||    ||||   | |    |||||||||||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || ||||| || |||||||| |
gtatatatatggctgtgaatctgtaaatatt-atcccagtcttttcat-gtacgtgtgttcaacatatttctgaaatgaattct-tctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtgaatggctaagatgcaccttctatttatttt-atatttttcgttgtttcca--tgacatgatttcatctgactaaaatttgatgtc-ctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
|| |   |||   |      | |  ||| | || || | |||  |||||             || |  || ||||   |  |  | |  ||  ||||||| ||||| || || || || |||||||||||||||||||| ||||| || |||||||| || |||||||||||||||||||| || |||||||| |
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
--------------gtgaatggctaagatgcaccttc-tatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
               | | | | | ||||| || ||  | || || | |  | ||| | || |||     |||| |   | ||| | |    ||  |       ||||||| || || |||||||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||||| |||||  | || ||||||||||||||||
gtgctaatttattgtttatttgtttagatgaacattagttttcatgtgacgtattttgatgattct----catggtgcaacctgtccatg--ttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
----------gtgaatggctaagatgc-----accttctatttattttatatttttcgttgttt-ccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
           |   |  || | | ||     ||  | |||| |  |    |  |||| || ||  | ||    |||||  | |   |  || |||    |    |||||||||| || ||||| || |||||||||||||||||||| || ||||| ||||| ||||| || || || |||||  | || |||||||| |||||||
ccgccagtgtattgtttactcaaacgctaagtactgtgtattcacgtggcctacttcgatgcttatcgtggtgcgattt-gttta--tggaacttgtgagc----agATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC

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|193354654|gb|FK323306.1|FK323306
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193636108|gb|FK583025.1|FK583025
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|16277955|gb|BI942651.1|BI942651
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193349576|gb|FK316132.1|FK316132
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|207752335|gb|GD725784.1|GD725784
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|37994041|gb|CF805787.1|CF805787
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193366672|gb|FK331974.1|FK331974
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193563010|gb|FK521823.1|FK521823
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|207737354|gb|GD716938.1|GD716938
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193607438|gb|FK558283.1|FK558283
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|151405667|gb|EV275481.1|EV275481
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAA
EST: gi|192301329|gb|FG990219.1|FG990219
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGT-CGTGA-CTATTTCAG                         ATGGCC-GCTCTA-GA-G-CATGCAT-GTGTTTTT
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTT
EST: gi|193354208|gb|FK319808.1|FK319808
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193646525|gb|FK587412.1|FK587412
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTT-GATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193438321|gb|FK400030.1|FK400030
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|193364162|gb|FK332208.1|FK332208
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGNGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|208325876|gb|GE123310.1|GE123310
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGGAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
EST: gi|21601986|gb|BQ612317.1|BQ612317
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgaatggct ... tgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC
                                             tgtcctct  CT-rich tract
                                   taaaatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatggctaagatgcaccttctatttattttatatttttcgttgtttccatgacatgatttcatctgactaaaatttgatgtcctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG