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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaccttttcttttctcctttatttctcatttgtatcttcatttaccttttcctttgtatatcaactctagccattcttttcctcatttattttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCATGCCTTAGTCCGGGATCTGGAAGAAGATGTCATTCGGCTGGAGCAGTTT

Basic information

species Glycine max
transcript GLYMA20G36110.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G074351_T02 (Zea mays), 3'ss of exon 11
tttaccttttcttttctcctttatttct-catttgtatcttcatttaccttttcctttgtatatcaactctagccattcttttcctcatttattttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCATGCCTTAGTCCGGGATCTGGAAGAAGATGTCATTCGGCTGGAGCAGTTT
|  || |      || ||     ||| | ||  |  ||     | | |      | |    | |||  ||||||   | || || |   ||   ||  |||||||| |||    || || ||||| ||||||||||||||||| ||||||||| |  |  |||| |||   || | ||| ||     | ||||| |  |||
tacacatagaaaattatctagcgtttgtgcacctagattgatctgttctgacagcatctgttctcatttctagcatctgttctcatttcttgccttg-cagGTTTGCTGGGCAGCAAATCCATGCGAGTGAAGATGATGGTTCTGTTAACCATACTCTTATCCGTGATTACGATGCAGAGGTGTCAAGACTGGACCGATTT

upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0220g00010.t01 (Vitis vinifera), 3'ss of exon 9
----tttaccttttcttttctc---ctttatttctcatttgtatcttcatttaccttttcctttgtatatcaactctagccattcttttcctcatttattttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCATGCCTTAGTCCGGGATCTGGAAGAAGATGTCATTCGGCTGGAGCAGTTT
    |||   |||  |   |     | |  ||| |  || ||     ||    |||  || ||||    | || | ||   | |||  |  |     |||    |||||||||||| || ||||||||||||||||||||||||||||| || ||||||||||| || ||||||||||| | |||||     |||||||||   |||
agggtttctgtttaatgagcatgagcatggtttttggttcgttgaaccaggatcctaatcatttgc---ttaattgtaatgaatctgattgtttccaatt----cagGTTTGGTGGAAGGCAGATACATGCCAGTGAAGATGATGGTTCTGTCAACCATGCCTTGGTGCGGGATCTGGACGCAGATGCTGAACGGCTGGAGGCATTT
















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|5688095|gb|AI941110.1|AI941110
EST:     AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG                         GTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
genomic: AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATGgtaattatat ... attttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
EST: gi|9984040|gb|BE658148.1|BE658148
EST:     AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG                         GTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
genomic: AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATGgtaattatat ... attttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
EST: gi|22928101|gb|BU545240.1|BU545240
EST:     AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG                         GTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
genomic: AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATGgtaattatat ... attttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
EST: gi|19052889|gb|BM731556.1|BM731556
EST:     AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG                         GTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
genomic: AAGGATAGGAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATGgtaattatat ... attttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA
EST: gi|213611162|gb|DB975008.1|DB975008
EST:     GAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATG                         GTTTGGTGGTAGACAGATACATGACAGTGAAGATGATGGTTCGGTTAACCA
genomic: GAAGGATGCCCAAAAGTGCATAGAATTGATGAACGGACGATGgtaattatat ... attttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttcctttgtatatcaactctagccattcttttcctcatttattttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCATGCCTTAGTCCGGGATCTGGAAGAAGATGTCATTCGGCTGGAGCAGTTT
                           ccattcttttcctcat  CT-rich tract
                                       tcatttattttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaccttttcttttctcctttatttctcatttgtatcttcatttaccttttcctttgtatatcaactctagccattcttttcctcatttattttatcagGTTTGGTGGTAGACAGATACATGCCAGTGAAGATGATGGTTCGGTTAACCATGCCTTAGTCCGGGATCTGGAAGAAGATGTCATTCGGCTGGAGCAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - -cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactct