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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAGGTGTGACACCCTCGTTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattttaacctaaaatatccgacttaaataacatttatttcaactgttgctttaaccaagtttggcgaacaacag

Basic information

species Glycine max
transcript GLYMA17G02640.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 23
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 23
------------AAGGAGGTGTGACACCCTCGTTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattttaacc----taaaatatccgacttaaataacattta--tttcaac-tgttgctttaaccaagtttggcgaacaacag-------------------------------------
             |||||||| || |||||| |||| || || |||||||| || ||||||||||||||| | |||||    ||  | ||||| |||||  ||| |  ||     | | ||| ||      |      ||    | |  | | | | |  |   ||| | ||||  ||       |       |||                                        
CCAAGAGCTAGCTAGGAGGTGCGAGACCCTCATTCGTCTAGTGGAGAAGGAGAACCAAGAATATGATGAGCGTGAGAGATTGGCCAGGAAAGATAAGAAGgttggtcatagtagacctttttcaattcccgtttggcttctagttcacttcatagtgaagtacaaacatattgccctagtagtcatcacaatgcaatctttctaatcttcagttttttactttcttgcacttgcag

upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 23
lower sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 15
---AAGGAGGTGTGACACCCTCGTTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattttaacctaaaatatccgacttaaataacatttatttca--actgttgctttaaccaa-gtttggcgaacaacag-----------------------------
    ||| ||||||| |||||  | || ||||| ||||| |||||||||||||||||||||   |||||||||||  | || ||||| |   |||||        || ||   | |      |      | |         || |||     | |   |   || | || |||    |     ||                              
GGCTAGGCGGTGTGATACCCTTATCCGACTGGTTGAGAAAGAAAATCAAGAATATGATGAGCAAGAGAGGCAAGCAAGGAAGGAGAAAAGGCTTGCTAAGgcaaatcctaaacttattcgctactcatcattgtgcagctcttcattatgtcattaaagacctagctaatgttatagggtttgcaatgatctgacatcaaacttgatatcaacag

upper sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 23
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 23
---AAGGAGGTGTGACACCCTCGTTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCT--GCTAAGgtt--cgtattttaacctaaaatatccg--acttaaataacattta--------tttcaactgttgctttaaccaagtttggcgaacaacag----------------------------
   ||| || ||||| |||||| ||||  | || |||| |||||||||||||| ||||||||||||||| || || || |||||||||||  ||||   | || | ||  | || |||  |||| |   |||   | || |  |  |||||        ||  |  | || | | ||  |  | |     |  | ||                            
TGCAAGAAGATGTGATACCCTCATTCGATTAGTGGAGAGGGAAAATCAAGAATTTGATGAGAGGGAGAGACAGGCACGGAAAGAGAAGAAGCTTGCCAAGgtatgattatcttactttgtcctagatgttcctgtattttatgattatttacactccttttggatttattacctaaataatatgtaattgatcaaagttcatctactcaactcctgaaatttcag

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|208034280|gb|GD833350.1|GD833350
EST:     ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAACTTGCTGCTAAG                         AGCATGACCCCGTCGAAGCGTTCCATGCCTAGACAGACTGAGAG
genomic: ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAG
EST: gi|23734541|gb|BU765507.1|BU765507
EST:     ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
genomic: ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
EST: gi|13790494|gb|BG653094.1|BG653094
EST:     ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
genomic: ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
EST: gi|6718901|gb|AW306548.1|AW306548
EST:     ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
genomic: ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
EST: gi|31468447|gb|CD410475.1|CD410475
EST:     ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
genomic: ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
EST: gi|193645408|gb|FK590824.1|FK590824
EST:     ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGCGAGAGTCCATCT
genomic: ATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
EST: gi|9984215|gb|BE658323.1|BE658323
EST:     GGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
genomic: GGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
EST: gi|5666945|gb|AI930981.1|AI930981
EST:     GGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAG                         AGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT
genomic: GGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattt ... cgaacaacagAGCATGACCCCATCGAAGCGTTCCATGCCTAGACAGAGTGAGAGTCCATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGAGGTGTGACACCCTCGTTCGGCTGGTAGAGAAGGAAAATCAAGAATATGATGAGAGGGAGAGGCAAGCTCGTAAAGAGAAGAAAATTGCTGCTAAGgttcgtattttaacctaaaatatccgacttaaataacatttatttcaactgttgctttaaccaagtttggcgaacaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT