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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag

Basic information

species Glycine max
transcript GLYMA05G03270.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 5'ss of exon 21
------------TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag
            ||| ||  |||||||||| || || ||||| ||||||||| | || || ||||||||||| ||| |||||||||| || ||||||||  | ||     ||  ||   |||      |    |  | ||   || |   |      | | |  ||| ||    ||||  |||||||    |||  |  | |||
AATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGTCAATGTCAAGGgtaac-----agaatatccttgaaaagtt---ggactctaccaatttatacacgg--aatctcttgttca----aacttgtgttctt----ctcaatattgcag

upper sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag
||| || ||||||||||| || || ||||| ||||| ||| | || |  ||||||| ||| |||||||||||||| || |||||||| || || |||||||| |       | || |  ||   | ||  ||| | ||       |  ||  | |       ||||  |||||||    ||   | || |||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgattt-acacacgggatcttttttt-----caaacttgtgttctt----cttaatactgcag

upper sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgt-------ccctctccaagtgtatattgatctc-acctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag
||| ||||||||||| || || |||||||| || |||||  | ||||||||||||||||||||||||||||| ||||| |||||||| || || ||||||||||   |||        |    |     | |   |||||||| |   |   | |||   | |   | ||    |  |||  |   | |  ||| | |||
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattgataagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

upper sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 18
lower sequence: EFJ31084 (Selaginella moellendorffii), 5'ss of exon 9
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag
|||||| || ||||||||||| || ||||| || |||||  | ||||| || ||||||||||| |||||||| ||||| ||||| |  ||| | ||||| || |    |  ||   |   |||||  |  | |  |   ||| ||  || || |                                      
TGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTTCAATGTCCACAATTGCATCTAAAgtaagcacttaccacgtgatagtgttcaa-gtttaccgttttctttcttcgcag--------------------------------------

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|17022161|gb|BM093195.1|BM093195
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|27425980|gb|CA937500.1|CA937500
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|26268110|gb|CA819173.1|CA819173
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|10844689|gb|BF067915.1|BF067915
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|207835662|gb|GD805659.1|GD805659
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAATATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|192328312|gb|FK020023.1|FK020023
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGCATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|26048337|gb|CA784840.1|CA784840
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
EST: gi|208092591|gb|GD885568.1|GD885568
EST:     AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAATATTACCTCTAAG                         TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT
genomic: AAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttg ... tttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTTCTATGTCAAGTATTACCTCTAAGgttaaatttgtccctctccaagtgtatattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcag

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