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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttggattacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag

Basic information

species Glycine max
transcript GLYMA02G07910.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 9
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtt--tggattacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag
 |||||||| || || || || ||||| ||| |||| || || ||||||||| | ||||||||||||||||| || |||||||| ||||| ||||||||||||    | | |     |   |  | | | || |  ||             | ||   | || | ||| |||    ||| | |    | ||||     ||  ||     | ||| || |                                                                       
AGGTGGAAACTCAGTGGCTACGGTTGTCTTAAGAGGCAGCACCGATAGTATATTGGATGATCTTGAAAGAGCTGTTGATGATGGTGTGAATACTTACAAGgtatgactgtaaatcaacttcctgtcattgttttggaa-------------catacatgctactcttattta----attagctaacaggttacctgactgttgg-----tgtttatacag----------------------------------------------------------------------

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 9
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttgga-ttacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag
 ||||||||||| || || |||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || |||||||||  | |  ||  | |  |   | |  | || |   | |    |        |  |  ||  |  |   |  ||  | |   ||   ||    |||  |                                                                                         
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactc-ttttattgtattgtaacgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag----------------------------------------------------------------------------------------

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 9
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttggattacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag
 ||||||||||| || || |||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || |||||||||  | |  ||  | |  |   | |  | |       || |    | ||   |  | ||   | || || ||      | || |  || | || |     |   ||  || ||  |  |||| |   |                                                           
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactctttt-------attgtattgtaacgttctgtgtctgttttgctaat-----ctattcgagtt-ctcact-----gtccttgtttattctagtcaatgtgcag-----------------------------------------------------------

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G381744_T01 (Zea mays), 5'ss of exon 9
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttggattacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag
 ||||||||||| || || ||||||||  |  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || |||| ||||  | | |  | | |        ||||       | ||  | |   |  | |  |   |||||| || |   |  | ||||| | | |   ||   |        | |||||  | || |                                                                  
TGGTGGAAATTCAGTGGCTACTGTTGTCCTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACATACAGGgtatgtctgtggtatcta-------taat-------agatgcgacctaattcttttgttgtattgtaacatcc-atgtctgtttagctaatctatccaagttctcactgtttttttatactag-----------------------------------------------------------------

upper sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 9
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttggattacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag
 |||||||| || |||  |||||| ||||||||||||||||||||||||||| ||||||| |||||||||||||| ||||| || ||||| || |||||||||| |||  |||   | | |    |  ||||||||| |||||      | |   | ||  | || |  ||    ||| | ||      ||   ||||  |||| |||||      ||   |||   ||||||     |||  |||   |                                      
AGGTGGAAACTCCGTATGCACTGTGGTTTTACGAGGAAGTACTGATAGTATATTAGATGACCTTGAAAGAGCAGTTGATGACGGTGTGAATACATACAAGgtaaattttatat---tggatgggctggtcttgtaaatataggtttttgagcactatgg--agtggtggttgcatcatctctt------acttttttgttggaaatttatgacgttaa--tattaggtgctttac---atttcaatgccag-------------------------------------

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|151397877|gb|EV267750.1|EV267750
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
EST: gi|193514452|gb|FK467940.1|FK467940
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
EST: gi|193420636|gb|FK390559.1|FK390559
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGAATAGCCGCTTTGTAC
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGA-TAGCCGCTTTGTAC
EST: gi|209700024|gb|BW656205.1|BW656205
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
EST: gi|193347893|gb|FK312785.1|FK312785
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGACAGGGATAGCCGCTTTGTAC
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTG-CAGGGATAGCCGCTTTGTAC
EST: gi|14011960|gb|BG726882.1|BG726882
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
EST: gi|193427201|gb|FK393451.1|FK393451
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTAC
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTAC
EST: gi|209728114|gb|BW655349.1|BW655349
EST:     ACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: ACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
EST: gi|298187661|gb|HO034810.1|HO034810
EST:     TACTACATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
EST: gi|254342218|gb|GR853355.1|GR853355
EST:     TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAG                         GCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT
genomic: TACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttct ... tacttgtcagGCAATGTGCAGGGATAGCCGCTTTGTACCTGGAGCTGCAGCTACTGAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttggattacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA