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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatcattatatcttaagcttaattaattacatctagctactttttcttttcactcatggaaatcattgttttgaaaactaatcaataatacatacatgccattaatttgttggctattctaatgtgttggcgcgcatctttttatgtactttcag

Basic information

species Glycine max
transcript GLYMA20G35270.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 4
GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgt--atgcatcattatatcttaagctta---attaattacatctagctactttttcttttcactcatggaaatcattgttttgaaaactaatcaataatacatacatgccat-taatttgttggctattctaatgtgttggcgcgcatctttttatgtactttcag
|||||||||||| ||||||||||| ||  | |||||||| ||||||||||| ||||| ||||||   ||||| || |  | |||    ||   |  |||||  ||    |   |||  |||| | |   ||      ||   ||| | |  | | | | | | |    ||  || |||| | ||   | || | |  ||||   |                       
GATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTGgtcagtgcat-atcaagttttatttctacatacaaattagctcct-ttgggtttgattttaagttggggtttaatttaagttggatatcagttactgacagaacagtgaaatataatatattttttgttttgaattgtttcag-----------------------

upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G14550.1 (Arabidopsis thaliana), 5'ss of exon 4
GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatcattatatcttaagcttaattaattacatctagctactttttcttttcactcatggaaatcattgttttgaaaactaatcaataatacatacatgccattaatttgttggctattctaatgtgttggcgcgcatctttttatgtactttcag
||||||||| ||||||||||| ||| |||| |||||||| ||||| ||||| ||||| ||||||| |  |  || | | ||    |  || | |  |      ||  | | | ||| || | |||    |  || ||||  |                                                                                
GATGTTTGTCGAGTCATGCAAACGTTTGCGCATAATGAAAGGATCCGAAGCAATTGGACTTGgtaagttttcttttctgttcgtttctataagtggct-----cttttctgtttttccaataatgctcgtgtttttttttcag-------------------------------------------------------------------------------

upper sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatcattatatcttaagcttaattaattacatctagctacttttt---cttttcactcatggaaatcattgttttgaaaactaatcaataatacatacatgccatt--aatttgttggctattctaatg-----tgttggcgcgcatctttttatgtactttcag--------------------
|||||||||||| |||||||||||  |||| |||||||| ||||||||||| ||||| ||||||| |||       | |   |  |   ||  |  | |  |   |  |  |   |  | || |||| ||       |  ||   | |   ||||   || ||  ||  || |  ||  | ||   |||| | ||      | ||  |    || |   ||| ||  |   |                    
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgca-tcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag

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:     GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAAAAGC
genomic: GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
EST: gi|12774194|gb|BG239121.1|BG239121
EST:     GTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCTGGCCTAATA
genomic: GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCGGGCCTAATA
EST: gi|14990435|gb|BI316108.1|BI316108
EST:     GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCGGGCCTAATA
genomic: GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGCTGAAGCGGGCCTAATA
EST: gi|10235874|gb|BE804762.1|BE804762
EST:     GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTG                         CTCCAAGAGCAATGGA
genomic: GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGA
EST: gi|4260448|gb|AI416944.1|AI416944
EST:     GTCATGCAAGCGTCTGCGAATAATGAAAGGATCAGAAGCGATTGGGCTTG                         CGCCAAGAGCAATGGGANAATGCAAAAGCAGAAGC
genomic: GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
EST: gi|9820436|gb|BE555946.1|BE555946
EST:     TCATGCAAGCGTCTGCGAATAAATGAAGG-ATCAGAAGCGATTGGGCTTG                         CGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
genomic: TCATGCAAGCGTCTGCGAATAA-TGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGCAAAAGCAGAAGC
EST: gi|10237183|gb|BE806071.1|BE806071
EST:     GTCATGCAAGCGTCTGCGAATAATGAAGGGATCATAAGCGATTGGGCTTG                         CGCCAAGAGCAATGGAAAAATGC
genomic: GTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatca ... gtactttcagCGCCAAGAGCAATGGAAAAATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatcattatatcttaagcttaattaattacatctagctactttttcttttcactcatggaaatcattgttttgaaaactaatcaataatacatacatgccattaatttgttggctattctaatgtgttggcgcgcatctttttatgtactttcag

- - - - - - - - - - - - - - - - - - - - - -  AGAAGC