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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagctgttattgatactggtgtaactaattgttaatacttggaccaattatcttactgatattttactgacttgttttttatgttgtgtttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCAT

Basic information

species Glycine max
transcript GLYMA20G38630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G51390.1 (Arabidopsis thaliana), 3'ss of exon 4
agagctgttattgatactggtgtaa-ctaattgttaatacttggaccaattatcttactgatattttactgacttgttttttatgttgtgt-ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCAT
                     ||||  |  || ||     |   | ||| | | | | | | ||   | | |  | || |  | | | | | ||||    || || ||||| ||||| || |||||||||||||| || || || || || ||||||||||| || ||| ||||||| || ||||| |||||||| ||||||
---------------------gtaagttttttatttgagttaaaagcaaatgt-tcaataagatcggatttatct-ttatcaaagctatttgttttggttagGGAAACTGGTATAGTGAAGCTTAGAATGCAAGGAGCTTGTAGCGGTTGTCCAAGTTCATCTGTTACTTTGAAATCCGGAATTGAGAATATGCTTATGCAT

upper sequence: GLYMA20G38630.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0106g00620.t01 (Vitis vinifera), 3'ss of exon 4
----------------------agagctgttattga-tactggtgtaactaattgttaatacttggaccaattatcttac-tgatattttactgacttgttttttatgttgtgtttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCAT
                      |||  |    |||| |  ||  || ||  | ||  | ||       |  ||  ||||  ||| ||| |  | | |||  |  ||||  || |  |||  ||| || || |||||||| ||||| | ||||||||| ||||| ||||||||||| || ||||| || || |||||||| ||||||||||||||||||||||| 
gtgagattcccttcatctagttagaagtaaagttgaatgttgaggtcac-gactgaaagtataaatttcttttcccttatatgacattgttttta-ttggatcatatgg-gtttacttcctcagGGAGACAGGAATAGTTAAACTAAAAATGCAAGGAGCATGTAGTGGCTGCCCTAGCTCATCTGTTACACTGAAATCTGGCATTGAAAATATGCTGATGCAC
















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|193412381|gb|FK381308.1|FK381308
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAAGAATGCAAGGGGCATGCAGTGGCTGCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTT-AGAATGCAAGGGGCATGCAGTGGCTGCC
EST: gi|208326189|gb|GE121985.1|GE121985
EST:     CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAA
genomic: CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAA
EST: gi|151408856|gb|EV278664.1|EV278664
EST:     CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAAGGGGC
genomic: CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAA-GGGGC
EST: gi|193544966|gb|FK504299.1|FK504299
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGTAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|207792627|gb|GD767389.1|GD767389
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|193630552|gb|FK584105.1|FK584105
EST:     CGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: CGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|193659389|gb|FK605972.1|FK605972
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|193411504|gb|FK381579.1|FK381579
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|193392603|gb|FK358762.1|FK358762
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|208051204|gb|GD846707.1|GD846707
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCC                         AGATACTGGAATAGCAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|193448629|gb|FK413354.1|FK413354
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|213591380|gb|DB959894.1|DB959894
EST:     CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGT
genomic: CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGT
EST: gi|208037729|gb|GD833643.1|GD833643
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|192327952|gb|FK021699.1|FK021699
EST:     CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTACCC
genomic: CCTGCAGTGCAAGATGATGGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|193328310|gb|FK294331.1|FK294331
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|208207238|gb|GE002119.1|GE002119
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
EST: gi|208025299|gb|GD822829.1|GD822829
EST:     GGCGGGGACATTGAATATAGAGGTTTTGACCT                         AGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC
genomic: GGCGGGGACATTGAATATAGAGGTTTTGACCTgtaagttccg ... ttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattatcttactgatattttactgacttgttttttatgttgtgtttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCAT
                    tactgac  putative branch site (score: 1)
                                       ttgtgtttttctcc  putative PPT
        ttactgatatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagctgttattgatactggtgtaactaattgttaatacttggaccaattatcttactgatattttactgacttgttttttatgttgtgtttttctccagAGATACTGGAATAGTAAAACTTAGAATGCAAGGGGCATGCAGTGGCTGCCCAAGTTCATCAGTGACTCTGAAATCAGGCATTGAAAATATGCTGATGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- -gctgtta
- - - - - - gatactg
- - - - - - - - - - - - - - - - - - - cttggac
- - - - - - - - - - - - - - - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg