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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtagtgtttgtgctttaagaattttttgtttctccagaataaaagttaattttggataacattattacaataccattatctacaatcattgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA

Basic information

species Glycine max
transcript GLYMA08G22740.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------ttgtagtgtttgtgc---tttaagaattttttgtttctccagaataaa--------agttaattttggataac--attattacaataccattatctac--aatcattg---tttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA
                                         || || ||||        |   |||||||| | | |||     |||||        | ||   |||||| |    ||||| |   |  ||| | || |  |||| ||    ||| ||||   |||||||| |||||||| | ||||||| | ||||||||| ||||||| ||||| |||||||||||||| ||||||  ||| 
gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataaatttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT
















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|22540175|gb|BU090018.1|BU090018
EST:     TCAGTGCTGCTGCTGGTGCAAACA-CAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: TCAGTGCTGCTGCTGTTGCAA-CAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|209725498|gb|BW677795.1|BW677795
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|17519381|gb|BM188423.1|BM188423
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|17400692|gb|BM177474.1|BM177474
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|10232087|gb|BE800975.1|BE800975
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|20448322|gb|BQ252446.1|BQ252446
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|151400172|gb|EV269986.1|EV269986
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|16105597|gb|BI893337.1|BI893337
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
EST: gi|213608233|gb|DB970830.1|DB970830
EST:     ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtacaaattc ... ttgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaattttggataacattattacaataccattatctacaatcattgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA
          ggataac  putative branch site (score: 3)
            ataacattattacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtagtgtttgtgctttaagaattttttgtttctccagaataaaagttaattttggataacattattacaataccattatctacaatcattgtttacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATAGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTTCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-tgtagtg
- - - - tttgtgc
- - - - - - - - - - - - - - - - -ctccaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatacc