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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattctaaatttgtgccttttcggtgaccaaatacttttgaacttagttaaactgaaggattataataaattcttaaattgtctcacttatgaatgttttattggttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTGGGAGTAGCCAGGACGTAGAGGAATTTGCCTGCACAAGATACAAGGCCGC

Basic information

species Glycine max
transcript GLYMA03G30800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G30800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattctaaatttgtgccttttcggtgaccaaatacttttgaacttagttaaactgaaggattataataaattcttaaattgtctcacttatgaatgttttattggttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTGGGAGTAGCCAGGACGTAGAGGAATTTGCCTGCACAAGATACAAGGCCGC
                                                                  |  ||   |   || |     | ||  |   ||| | |   ||||| |  |   | | | ||||  || | |  |||   || ||| || || |  ||||  |||||||  | |||||||||||||| || ||||||||||| |||||||||   ||  || | | | | |||||||| || |||||||||||||| | 
-------------------------------------------------------------atcatcaatttaattgacataagtcatagatttagattagattttgggatttttct---tccctgaatttgctgagtcttgag-attatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
















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|298192383|gb|HO036465.1|HO036465
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|213611742|gb|DB958864.1|DB958864
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|298165676|gb|HO008647.1|HO008647
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|298175980|gb|HO015385.1|HO015385
EST:     TACCAATTACACCCAGTTAACTGAGCCTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|16345172|gb|BI970767.1|BI970767
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|298194623|gb|HO043095.1|HO043095
EST:     TACCAATTACACCCAGTTAACTGAGCGTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|58023037|gb|CX709778.1|CX709778
EST:     TACCAAATACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|193553968|gb|FK512509.1|FK512509
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGG
EST: gi|8282815|gb|BE020376.1|BE020376
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|298178511|gb|HO024246.1|HO024246
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|298181386|gb|HO022825.1|HO022825
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|23734566|gb|BU765519.1|BU765519
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|18039234|gb|BM307528.1|BM307528
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|57574515|gb|CX547490.1|CX547490
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
EST: gi|17400959|gb|BM177741.1|BM177741
EST:     TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAG                         GCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG
genomic: TACCAATTACACCCAGTTAACTGAGCTTTACAGCAAATACAAAGACAGAGgtatggtttt ... ttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataataaattcttaaattgtctcacttatgaatgttttattggttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTGGGAGTAGCCAGGACGTAGAGGAATTTGCCTGCACAAGATACAAGGCCGC
     ataaattcttaaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattctaaatttgtgccttttcggtgaccaaatacttttgaacttagttaaactgaaggattataataaattcttaaattgtctcacttatgaatgttttattggttgatctcagGCCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAGCAGGAGCCTGGGAGTAGCCAGGACGTAGAGGAATTTGCCTGCACAAGATACAAGGCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA