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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgttaacaaagcttcttgttttggaagtttcaataaatatcaccacaatatttttattttcatgaattaatgttttgatgatgatgatgatgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCATTGATGGGTCAGCTTTTCCTGAATAAAACCATAGAGTGGTCAGAGTTTC

Basic information

species Glycine max
transcript GLYMA09G33160.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 9
acgttaacaaagcttcttgttttggaagtttcaataaatatcaccacaatatttttattttcatgaat-taatgttttgatgatgatgatgatgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCATTGATGGGTCAGCTTTTCCTGAATAAAACCATAGAGTGGTCAGAGTTTC
  || ||  ||  | ||| |  |      |   | || |       |  || | |   ||| |    | ||||    |||  ||  | ||  ||   | |||| ||||| || || ||   |||||| ||||| || |||||||| ||||||||| |||| ||||| ||||||||||| | |||||  |||||||| || |
-agtaaaggaatttccttataataatttgtcataaaagttctgtttctctagtctgcatttgaaatctataataagatgagaattttcattttggcaacagGTGGGACATCGAACTTATGAGAACTTGAAGACAATCAGGCCAAACATGGCATTGTTGGGCCAGCTCTTCCTGAATAAGAGCATAGGTTGGTCAGAATTCC
















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|22524223|gb|BU083034.1|BU083034
EST:     ATAGGGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|17964389|gb|BM271125.1|BM271125
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|58022401|gb|CX709142.1|CX709142
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|12496084|gb|BG046886.1|BG046886
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|6746807|gb|AW317263.1|AW317263
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|57574111|gb|CX547086.1|CX547086
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|209723949|gb|BW671596.1|BW671596
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|38192783|gb|CF921989.1|CF921989
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACGCCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|22524343|gb|BU083154.1|BU083154
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|19053704|gb|BM732371.1|BM732371
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|27425911|gb|CA937431.1|CA937431
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|18732773|gb|BM527240.1|BM527240
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|17401789|gb|BM178571.1|BM178571
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|6724485|gb|AW308884.1|AW308884
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|120530290|gb|EH258424.1|EH258424
EST:     CACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: CACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|16349513|gb|BI975108.1|BI975108
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|209698836|gb|BW675764.1|BW675764
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|192308464|gb|FK000932.1|FK000932
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
EST: gi|8286203|gb|BE023762.1|BE023762
EST:     ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTG                         GTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA
genomic: ATAGTGACATCTTCATCTCTGCTTCCCCAGGAAATATGCACAATGCATTGgtgagttgtg ... atgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatatttttattttcatgaattaatgttttgatgatgatgatgatgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCATTGATGGGTCAGCTTTTCCTGAATAAAACCATAGAGTGGTCAGAGTTTC
     atttttattttcatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgttaacaaagcttcttgttttggaagtttcaataaatatcaccacaatatttttattttcatgaattaatgttttgatgatgatgatgatgatgatagGTTGGACACCGGACATACTTGAACTTAAAGACTATAAGGCCAAATATGGCATTGATGGGTCAGCTTTTCCTGAATAAAACCATAGAGTGGTCAGAGTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - -gcttctt
- - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgatg