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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatcttatattaacaatttatctatgtttcgtgttcaagggtgttttcaatctatcactattaacacagtagtccttgatgattttactgccttttcccctccag

Basic information

species Glycine max
transcript GLYMA15G13190.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G13190.3 (Glycine max), 5'ss of exon 3
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 5'ss of exon 3
AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttg---taatcttatattaacaatttatctatgtttcgtgttcaagggtgttttcaatctatcactattaacacagtagtccttgatgattttactgccttttcccctccag
||||||| || ||||||||||| || |||||  | ||||| ||||||||||||||||  || ||  ||| | | |||||| | |||  |||||| || |||||    ||||| ||  || | | |||   ||| ||   | | ||        |||  || |  | | |  |        || |          | | |              
AAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTTAGCCAGTGTGCTTGAGGGACTCTTTGATGCAGTGACCCTTCTCCTTAGgtttgtctaatcatagcttcaaatttttgttatattatttctacattcccaacttcgctcaa--attttcgatcttcctctcttctgaacccaaattacag------------

upper sequence: GLYMA15G13190.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 5'ss of exon 4
AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatcttatattaacaatttatctatgtttcgtgttcaagggtgttttcaatctatcactattaacacagtagtccttgatgattt-tactgccttttcc--cctccag
|||| ||||||||||||||||| ||||||||  |||||||||| || |||||||| |||||||| || |  ||||||||| | || || ||||| || ||||  |  |   | | |||   ||  | |  |     | || |  |  |||   |   |    ||| ||| |    || | ||| |   |  |  |||||   |   | |||||
AAGACCTTCACTTCTTTGTTACTGGTGGTGAAGATGAAAATGAACTAATCTTAGCTACAGTTCTCCAAGGGTTTTTTGATGCAGTTGGTCTTCTCCTTAGgt-atctttcaagaataattgttactattagcaatctcttaattgaggttcagatgttgatgctagtaatatgtgagcctttgttatctaattttgcctgcccttgcttccag
















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|298178201|gb|HO023936.1|HO023936
EST:     TTAGCCACGGTTCTGCAGGCATTTTTTGGTTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298190231|gb|HO032352.1|HO032352
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGACCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|151408791|gb|EV278599.1|EV278599
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|192325778|gb|FK018000.1|FK018000
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|41145498|gb|CK605709.1|CK605709
EST:     TTACCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|58014334|gb|CX701076.1|CX701076
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|151408109|gb|EV277917.1|EV277917
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|192294109|gb|FG986198.1|FG986198
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298194358|gb|HO041006.1|HO041006
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|209704906|gb|BW661709.1|BW661709
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|8402161|gb|BE057795.1|BE057795
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|58017732|gb|CX704474.1|CX704474
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|23729019|gb|BU762586.1|BU762586
EST:     GTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: GTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|14258489|gb|BG881397.1|BG881397
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAAGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|5057863|gb|AI736339.1|AI736339
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298175562|gb|HO018273.1|HO018273
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298175469|gb|HO015102.1|HO015102
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|209704905|gb|BW661708.1|BW661708
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatct ... tcccctccagAGGCAATGTAGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtaatcttatattaacaatttatctatgtttcgtgttcaagggtgttttcaatctatcactattaacacagtagtccttgatgattttactgccttttcccctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG