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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagcttttacgactttgcatcttttgtgggtgataagttctttatgttacatatatatgcatgtatcaaacataggatgaacaagattgttgtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCATTCTCCTGACCCAAATTGTTATGCAAAG

Basic information

species Glycine max
transcript GLYMA11G05760.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 17
lower sequence: AT2G23380.1 (Arabidopsis thaliana), 3'ss of exon 15
gcaagcttttacgactttgcatcttttgtgggtgataagt-tctttatgttacatatatatgcatgtatcaaacat-aggatgaacaagattgttgtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCATTCTCCTGACCCAAATTGTTATGCAAAG
          ||| ||  ||| ||||     ||   || | ||||| | |    | | || |      |||||  | |  |||     |    ||||   |||||||||| || ||||||||| | || || |||||| |||| || || |||||||||||||| || || ||||| ||||||
--------gcacgtctcagcagctttgaaatgtcccaactctctttctctctagtctctaggttgtcttcaaattttaaaatgtttttgg--attgtgc-tgcagTTTGTGCTAGATGCTTACAGGAAAGGAGATAAACTGAAATTCGCCAACCATTCTCCTGAACCTAACTGTTACGCAAAG

upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 13
--gcaagcttt-tacgactttgcatcttttgtgggtgataagttctttatgttacatatatatgcatgtatcaaacataggatgaacaagattgttgtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCATTCTCCTGACCCAAATTGTTATGCAAAG
    |  ||   ||| || ||  |  ||| ||     | |   | | ||| || ||| | |     || ||  || ||| ||    |||||||  | | | ||||||||||||||||||| ||  |||| ||||| |||||||||||||| ||||||||||| || || ||||| |||||||||
gcatatactcaatacaacctttgaa-tttggtttaaaacatactttctattttccattttt-----tgaatagaa-atatgaattgcaagattactttttctgcagTTTGTTCTTGATGCCTATAGAAAAGGTGACAAATTGAAGTTTGCCAACCATTCTCCAGATCCTAATTGCTATGCAAAG
















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|208232711|gb|GE029944.1|GE029944
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATA
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATA
EST: gi|23063121|gb|BU578542.1|BU578542
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
EST: gi|14990221|gb|BI315894.1|BI315894
EST:     TTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: TTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
EST: gi|22932691|gb|BU549830.1|BU549830
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
EST: gi|6913222|gb|AW394752.1|AW394752
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
EST: gi|208261748|gb|GE059515.1|GE059515
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
EST: gi|254325926|gb|GR838807.1|GR838807
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
EST: gi|254327703|gb|GR834668.1|GR834668
EST:     AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAG                         TTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT
genomic: AGATATATGACCGTGAAAATTCATCTTTTCTCTTTAATTTGAATGATCAGgcaagctttt ... gtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatatatatgcatgtatcaaacataggatgaacaagattgttgtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCATTCTCCTGACCCAAATTGTTATGCAAAG
     tatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagcttttacgactttgcatcttttgtgggtgataagttctttatgttacatatatatgcatgtatcaaacataggatgaacaagattgttgtatatgcagTTTGTTCTTGATGCTTACCGAAAGGGTGATAAATTGAAGTTTGCGAACCATTCTCCTGACCCAAATTGTTATGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG