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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcagaaacgtatatacttaggcattaattattcttatactgtattttaattctgtaaacccacgaaataaaccttaattaactgtttaattttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG

Basic information

species Glycine max
transcript GLYMA20G35270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35270.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------atcagaaacgtatatacttaggcattaat-tattcttatactgtattttaattctgtaaacccacgaaataaaccttaattaact-gtttaattttctgaa-----gGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG
                                                 ||   ||     |  | | ||| | || | |     | |  | |   |  || || |  | |   |   | ||   | |  |  | ||||     |   ||     ||||||||||||| ||||||||||| ||  | |||||||| ||||||||||| ||||| ||||
gtcagtaatctctacttaaattttctattatctaatatctaagtgtttaattttaataacctgaattaaggtactagtctgaatctctgatatgagtccatgctctgcatctgtgttctgaattctgaccattttgtttggaaatggaaatttcagGATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTG

upper sequence: GLYMA20G35270.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14550.1 (Arabidopsis thaliana), 3'ss of exon 3
--atcagaaacgtatatacttaggcattaattattcttatactgtattttaattctg-taaacccacgaaataaacc-ttaattaactgtttaattttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG
   | |   |   ||||  |    ||||  |   |   | |   | ||| | ||    || |      || | |  |   ||   |       ||||     ||||||||||| ||||||||||| ||| |||| |||||||| ||||| ||||| ||||| ||||
tactaactcatcaatatgttacctcatttgtagctggcacatattctttcactttcaatagatttctaaatttagtcaccaacccaaatcccgatttc----agGATGTTTGTCGAGTCATGCAAACGTTTGCGCATAATGAAAGGATCCGAAGCAATTGGACTTG

upper sequence: GLYMA20G35270.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g04690.t01 (Vitis vinifera), 3'ss of exon 3
-atcagaaacgtat-atacttaggcattaattattcttatactgtattttaattctgt--aaacccacgaaataaaccttaattaactgtttaattttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG
    ||     ||| ||   || |  | || |  ||  ||     | |  |||||     ||| | | ||  ||||  ||||    |||||| ||||  || |||||||||||||| |||||||||||  |||| |||||||| ||||||||||| ||||| ||||
ttgtagttggttatcatctatatgggtaaaattctcacatgaaacaataaaattccaccaaaagctatgac-taaagtttaa---gctgtttgatttcatgcagGATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG

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|7924350|gb|AW830376.1|AW830376
EST:     TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
EST: gi|12774194|gb|BG239121.1|BG239121
EST:     TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGC
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
EST: gi|14990435|gb|BI316108.1|BI316108
EST:     TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
EST: gi|10235874|gb|BE804762.1|BE804762
EST:     TATGAAGATAATGATGGTGACTGGATGCTCCTGGGTGATGTCCCATGGGA                         GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
EST: gi|4260448|gb|AI416944.1|AI416944
EST:     TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAAGGATCAGAAGC
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC
EST: gi|12774381|gb|BG239308.1|BG239308
EST:     TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         GATGTTTGTTGAGTCATG
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATG
EST: gi|9820436|gb|BE555946.1|BE555946
EST:     TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAAATGAAGG-ATCAGAAG
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAA-TGAAGGGATCAGAAG
EST: gi|10237183|gb|BE806071.1|BE806071
EST:     TATGAATATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGA                         TATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCATAAGC
genomic: TATGAAGATAAGGATGGTGACTGGATGCTCGTGGGTGATGTCCCATGGGAgtaagttctt ... ttttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattctgtaaacccacgaaataaaccttaattaactgtttaattttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG
                                             ttttct  CT-rich tract
                    aaataaaccttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcagaaacgtatatacttaggcattaattattcttatactgtattttaattctgtaaacccacgaaataaaccttaattaactgtttaattttctgaagGATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa