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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactttacttcccctattatatactaatagggtattctcttctgtgaaatgaagttttaggctatgatctggtgtataaaattgtgagtttctatttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG

Basic information

species Glycine max
transcript GLYMA04G08200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G08200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g02850.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtgactttacttcccctattatatactaataggg-tattctcttctgtgaaatgaagttttaggctatgatctggtgtataaaattgtgagtttctatttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG
    || | ||  | |    |   ||  | || | ||| ||||  ||    ||||   |   |     || |  | |   ||| | |||| |      ||  || || || ||||| ||||| || ||||| || || ||||||||||||||||||||| | ||| | |||||||| || |||
--gcgtcatttggcatttattgccatgcaatatttgggatattagctaacttgaagccacaatcatacctgt--ttttaagtaaacaattat------cttcttgtgcagGATACAGCTTGGGCAGCCTGCGACTGTCAAAGTTGCTGCAAACCTTGTCAGGCTTGTATCATATAATAACAAG
















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|10709899|gb|BF009623.1|BF009623
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|58022364|gb|CX709105.1|CX709105
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|58022573|gb|CX709314.1|CX709314
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|19934684|gb|BQ079714.1|BQ079714
EST:     CTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: CTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|58016325|gb|CX703067.1|CX703067
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|298174239|gb|HO017575.1|HO017575
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|23730341|gb|BU763264.1|BU763264
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|254320192|gb|GR829380.1|GR829380
EST:     TTCCTCCATCAACACCC                         AATACAACTTGAACAACCTGCAACAGTTAAAGTTGCTGC-AACCTTGTCCG
genomic: TTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|254320191|gb|GR829379.1|GR829379
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|213619813|gb|DB969477.1|DB969477
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|33388670|gb|CA851877.1|CA851877
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|298192887|gb|HO033321.1|HO033321
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGGCAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|15813603|gb|BI785878.1|BI785878
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
EST: gi|58019397|gb|CX706139.1|CX706139
EST:     GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACAC                         AATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG
genomic: GATTCTCAGATTGTCTCTGATTATGTGCGTTACTTCCTCCATCAACACACgtaagtgact ... atttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaagttttaggctatgatctggtgtataaaattgtgagtttctatttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG
                                        tttctattt  CT-rich tract
                                        tttctatttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactttacttcccctattatatactaatagggtattctcttctgtgaaatgaagttttaggctatgatctggtgtataaaattgtgagtttctatttatgtagAATACAACTTGGACAACCTGCAACAGTTAAAGTTGCTGCAAACCTTGTCCGACTTCTCTCATATAACAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC