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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCAGCTAAGGCAGACAAGCTGTCTGCTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAGgtgacatttttaccttctctctatctctgtcttgcatatcttttatgctgatagggactattcattttgaaatattagttattcttatgaaacagagaggtaaagcatagttggattgaattggatattttgtag

Basic information

species Glycine max
transcript GLYMA20G35310.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35310.1 (Glycine max), 5'ss of exon 20
lower sequence: AT5G02940.1 (Arabidopsis thaliana), 5'ss of exon 18
ATCCAGCTAAGGCAGACAAGCTGTCTGCTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAGgtgacatttttaccttctctctatctctgtcttgcatatcttttatgctgatagggactattcattttgaaatattag-ttattcttatgaaacagagaggtaaagcatagttggattgaattggatattttgtag
||||| |||  |||||||| |  ||||||||| |||| |||||||||||||  ||||||||||| ||||| ||||||||    ||  |  ||  |    | |    |  ||| ||     ||| ||  |     |         |||| | | |  ||| | || |         ||                                    
ATCCATCTAGAGCAGACAAACAATCTGCTTATACTCTTCTCCTTGCTGAAACCATCTGCAACAAGCTTGGAGTTAAGgtagtgttagtgactatt----aacctcataatgc-tactgcctatactattcacatcctacttcactgaactttcatcttactattgttgtttctttag------------------------------------

upper sequence: GLYMA20G35310.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv05s0020g04630.t01 (Vitis vinifera), 5'ss of exon 19
ATCCAGCTAAGGCAGACAAGCTGTCTGCTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAGgtga---catttttaccttctctct--atctctg-tcttgcatatcttttatgctgatagggactattcattttgaaatattagttattcttatgaaacagagaggtaaagcatagttggattgaattggatattttgtag
||||  | | ||| ||||| |  ||||| |||||||| || |||||||||||||| |||||||||||||| || |||||||     |||| |  ||   | |  | ||||  || |   ||| | |     |  | ||   | || | |   |  |||  || || ||| | ||                                            
ATCCGTCCAGGGCGGACAAACATTCTGCATATTCTCTGCTTCTTGCTGAAAATATTTGCAACAAACTTGGAGTGAAGgtgagcatgttttcaggtttaatttgaacctctactcatagttatatctataaatctttggcttttttgagtaatacttataggtgatccttcttaagtg-----------------------------------------
















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|10233542|gb|BE802430.1|BE802430
EST:     CTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAG                         GTGCAAAATCTAGTTGCAGAAATTGTTGATTCAAAATTGGGGAAACAA
genomic: CTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAGgtgacatttt ... tattttgtagGTGCAAAATCTAGTTGCAGAAATTGTTGATTCAAAATTGGGGAAACAA
EST: gi|7028907|gb|AW458690.1|AW458690
EST:     CTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAG                         GTGCAAAATCTAGTTGCACAAATTGTTGATTCAAAATTGGGGAAACAA
genomic: CTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAGgtgacatttt ... tattttgtagGTGCAAAATCTAGTTGCAGAAATTGTTGATTCAAAATTGGGGAAACAA
EST: gi|209723743|gb|BW657725.1|BW657725
EST:     GCAACAAACTTGGGGTTAAG                         GTGCAAAATCTAGTTGCAGAAA-TGTTGATTCAAAATTGGGGAAACAA
genomic: GCAACAAACTTGGGGTTAAGgtgacatttt ... tattttgtagGTGCAAAATCTAGTTGCAGAAATTGTTGATTCAAAATTGGGGAAACAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCAGCTAAGGCAGACAAGCTGTCTGCTTATTCTCTCCTCCTTGCTGAAAATATCTGCAACAAACTTGGGGTTAAGgtgacatttttaccttctctctatctctgtcttgcatatcttttatgctgatagggactattcattttgaaatattagttattcttatgaaacagagaggtaaagcatagttggattgaattggatattttgtag

- - - - - - - - - - - - - - - - -  CTCCTC