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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaacaactttcaaaatccagacttatggtcttgtcttgtgttaactattttatagaattatctcaccagtcaccacagcctggctgttcttgtgcttttggcttgaatgtttaaattacatagttattagtattggcatatcttgagaaactctatgtatgattgccctgatgatcataccctggccattgcag

Basic information

species Glycine max
transcript GLYMA09G24630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G24630.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os10g38970.1 (Oryza sativa), 5'ss of exon 3
GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaacaactttcaaaatccagacttatggtcttgtcttgtgttaactattttatagaattatc-tcaccagtcaccacagcctggctgttcttgtgcttttggcttgaatgtttaaattacatagttattagtattggcatatcttgagaaactctatgtatgattgccctgatgatcataccctggccattgcag
| ||||||||| | |||||||||||||||||||| ||| ||| ||| ||||  || |||||| |   |||| |     | ||| |   | |  |||||||   |   |  || ||   | | || ||   | ||  |       |||     | || |||||  | || ||  |                                                                                              
GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAGgtatgc--ttattttaacttttcttacttatg-catcagcaagtttt---tctcttgtatgttcattgttgtgtagcacacactcttgcctgttggtatgtttaag----------------------------------------------------------------------------------------------

upper sequence: GLYMA09G24630.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0050g01050.t01 (Vitis vinifera), 5'ss of exon 3
GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaacaactttcaaaatccagacttatggtcttgtcttgtgttaactattttatagaattatctcaccagtcaccacagcctggctgttcttgtgcttttggcttgaatgtttaaattacatagttattagtattggcatatcttgagaaactctatgtatgattgccctgatgatcataccctggccattgcag
||||||| ||  |||| ||||||||||||||| |||| |||||||| || |||||||||||||| ||||| |||    |  | |   ||    | || |  | ||    ||    || ||| ||    || ||  |||    | |   |    | | | || | |      ||  |                                                                                           
GTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGGgtgagat---atctcctgcattttcatttgtcatattcaactgg---aattatatttacaaactagttcatttctaattgcta--taggtcttgtagaaacactgagt-------------------------------------------------------------------------------------------
















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|6341710|gb|AW164596.1|AW164596
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|192318263|gb|FK005795.1|FK005795
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|120495740|gb|EH223907.1|EH223907
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|151395908|gb|EV265785.1|EV265785
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|213606065|gb|DB980217.1|DB980217
EST:     CAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATCCCGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGCATCAGCAAGCAAAGTAGCATACCGG
genomic: CAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|15812897|gb|BI785172.1|BI785172
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|14258831|gb|BG881739.1|BG881739
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|31456764|gb|CD398792.1|CD398792
EST:     CCCATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|254331920|gb|GR843663.1|GR843663
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|9565795|gb|BE475304.1|BE475304
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|192318264|gb|FK005796.1|FK005796
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|16342588|gb|BI968183.1|BI968183
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|120495594|gb|EH223761.1|EH223761
EST:     CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaaca ... gccattgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaaacaactttcaaaatccagacttatggtcttgtcttgtgttaactattttatagaattatctcaccagtcaccacagcctggctgttcttgtgcttttggcttgaatgtttaaattacatagttattagtattggcatatcttgagaaactctatgtatgattgccctgatgatcataccctggccattgcag

- - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - -  GCTGGA