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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagattgagtcatgtagaaaggcatggtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

Basic information

species Glycine max
transcript GLYMA17G36540.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 16
-----------------------------------------atagattgagtcatgta--gaaaggcatggtaatctccctgcataaa-----aatcca-taagatttttcagcatttacatctacaaatctgctttatatgatt-----tcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
                                         |  ||   | |  || |   ||||| ||   | | ||  ||||  |       ||||| ||   |   ||  ||| |  ||    ||||   | || |    ||     | |||||||||||||||| ||||| |||||||| ||||||||||| || || || || || |||||||| || || |||||||| || || || ||||||||||
gtagatttaattttgcttgcattgacaattgaaccaaagaaaaggaacaaattttgaaccaaaaggaatacaactttctatgcagcagcttgtgatccagtatagtgcctcctcatattgattgcaaaatacaccttttgcctttctcttttagGAAGACTTCTATGCGGTTGTCGATTGGGCATACAAGATTGATCCCTTGCGTTGCATTTCAATGCATGGGATTACAGAACGATACCTGTCCGGTCAGAAAG

upper sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 16
---------------------------------------------atagattgagtcatgtagaaaggcatggtaatctccctgc-ataaaaatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
                                             |     |||    | |  || |  |   | |  || |||  |||  ||   ||  |  ||  ||   || |||| |     | |   ||||||  |||||||| |||||||||||| | || || ||||| | |||| | || || ||  | |||||||||||||| || |||||||| |||||||| ||||||||||| |
gttgatatttttggcatttccctttgtaaattggacagttatcctactatatgaactgt-tgaaatgataaaatgaaatcgctgtgataggaa---atggggcttcacaa-gttcacatgttt---tgtatcttatatt-tttcagGAGGACTTCTATGCTATAGTTGACTGGGCATTCAAGCTAGATCCATTGAGTTGTATATCAATGCATGGCATAACAGATCGCTATCTTTCTGGTCAGAAGG

upper sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 16
----atagattgagtcatgtagaaaggcatg-gtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
     |  |||      | |    | |      | ||    | | ||   | |    ||  |  |||||    |  |     |  | | |    |   ||| ||||||||||||||||| || || ||||||||||| || |||||||| || || || || |||||||| || || ||||| || || || ||||| |||||||
aattgtgcattcttctgttttttcatgtgcacattattgtgcagtattgcagttgccaacttccttcagtgactgaa-----atgttttcccccttgtattccagGAAGACTTCTATGCGGTCGTAGATTGGGCTTATAAAATTGACCCCTTGCGTTGCATCTCAATGCATGGGATTACAGAGCGTTACCTTTCTGGACAGAAAG

upper sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G060949_T01 (Zea mays), 3'ss of exon 4
atagattgagtcatgtagaaaggcatggtaatctccctgcataaaaatccataagattttt--cagcatttacatctacaaatctgctttatatgatt-----tcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
      ||  | || ||||     ||  | ||   ||   |    | |    || |||||   | || ||           |  || |||||||| ||     |||||| ||||| |||||| | || || ||||| | |||| | || || ||  | || ||||||||||| ||| ||||||| || ||||| |||||||||||||
------tgcataatttagactaa-atactgatgagccaagagctgagttaccaacattttgggctgcgttgttgagccttcacttgttttatatggttccttttcagGAGGACTTTTATGCTTTGGTTGACTGGGCATTCAAGCTAGATCCATTGAGTTGCATATCAATGCATGGACTAACAGATCGGTATCTTTCTGGTCAGAAAG

upper sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 16
atagattgagtcatg-tagaaaggcatggtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatc----tgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
   || |   | ||| ||    ||  |   ||  |     |  ||  | |   || | ||   ||  || ||      || |     |  ||||| |||||  |||||||||| ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||||||||| || || |||||||| ||| | |||||||||||||
---gact--cttatgctatggtggtttaccaagttaatctccaaagtaactccaaaaattccaagttttgactagcgaaatttgtcattttttatgtgattctagGAAGACTTTTATGCAGTGGTGGATTGGGCATACAAGATTGATCCTTTGCGCTGCATATCAATGCATGGGATTACAGAACGGTATATTTCTGGTCAGAAAG

upper sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 16
lower sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 16
atagattgagtcatgtagaaaggcatggtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
                                           |   || ||  |||||     | || || ||||        |   || || |||||||| || |||||||||||||||||||||||||||||  |||| |||||  | || || |||||||| || | ||||||||| ||||||||  |||| ||||
-----------------------------------------gtagcgtctatgtgattt-----cgttgacgtcta-------acacaatctg-tttcagGAGGATTTCTATGCTGTTGTGGATTGGGCTTACAAAGTTGATCCTTTGAGGTGCATCTCAATGCAAGGGACAACAGAACGATATCTCTCAAGTCACAAAG

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|208059885|gb|GD859063.1|GD859063
EST:     AGCTTGAAGCTTTGAATAAATCACTTAAGGATTTACTTGATGGAATACAA                         GAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTG
genomic: AGCTTGAAGCTTTGAATAAATCACTTAAGGATTTACTTGATGGAATACAAgtatgcataa ... atgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTG
EST: gi|192294049|gb|FG987218.1|FG987218
EST:     AGCTTTGAATAAATCACTTAAGGATTTACTTGATGGAATACAA                         GAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGC
genomic: AGCTTTGAATAAATCACTTAAGGATTTACTTGATGGAATACAAgtatgcataa ... atgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG
                                        tttatatgatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagattgagtcatgtagaaaggcatggtaatctccctgcataaaaatccataagatttttcagcatttacatctacaaatctgctttatatgatttcagGAAGACTTCTATGCTGTTGTGGATTGGGCTTACAAGATTGACCCTTTACGCTGTATATCAATGCACGGAATAACAGAACGCTATCTCTCTGGTCAGAAAG

- - - - - tcatgta
- - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - -tctccct
- - - - - - - - - - - - - - - - - - - - ataaaaa