Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtcttacataaacaatttatatatgttccatgttcaagggtgtttttaatctatcactattaacacagtagtccttgatgattttactgtcttttcccctctag

Basic information

species Glycine max
transcript GLYMA09G02270.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G02270.3 (Glycine max), 5'ss of exon 3
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 5'ss of exon 3
AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtcttacataaacaatttatatatgttccatgttcaagggtgtttttaatctatcactattaacacagtagtccttgatgattttactgtcttttcccctctag---
||||||| || ||||||||||| || |||||  | ||||| ||||||||||||||||  || ||  ||| | | |||||| | |||  |||||| || |||||   |||| |    | |  || | || | |   || ||        ||| ||    ||  | |    | |   | |  | |||  |  |    |||   |||   |     
AAGATCTCCATTTCTTTGTTACGGGCGGTGAAGAGGAAAACGAGCTTATCTTAGCCAGTGTGCTTGAGGGACTCTTTGATGCAGTGACCCTTCTCCTTAGgtt--tgtctaatcatagc--ttcaaatttttgttatatt-------atttcta---cattcccaacttcgctcaaattttcgatcttcctctcttctgaacccaaattacag

upper sequence: GLYMA09G02270.3 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 5'ss of exon 4
AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtcttacataaacaatttata-tatgttccatgt-tcaagggtgtttttaat-ctatcactattaacacagtagtccttgatg----attttactgtcttttcccctctag
|||| ||||||||||||||||| ||||||||  |||||||||| || |||||||| |||||||| || |  ||||||||| | || || ||||| || ||||     |||| ||  || ||||  || |||   | || | | ||  | | ||   ||  |    ||| ||| |    || | ||| |     ||||| |  |    |  | || ||
AAGACCTTCACTTCTTTGTTACTGGTGGTGAAGATGAAAATGAACTAATCTTAGCTACAGTTCTCCAAGGGTTTTTTGATGCAGTTGGTCTTCTCCTTAGgt----atctttcaagaataattgttactattagcaatctcttaattgaggttcagatgttgatgctagtaatatgtgagcctttgttatctaattttgcc-tgcccttgcttccag
















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|192332965|gb|FK024614.1|FK024614
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|120493426|gb|EH221593.1|EH221593
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|120492487|gb|EH220654.1|EH220654
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|14259369|gb|BG882277.1|BG882277
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298184953|gb|HO030166.1|HO030166
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|151410972|gb|EV280787.1|EV280787
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|151405407|gb|EV275221.1|EV275221
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298191889|gb|HO035971.1|HO035971
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|151410188|gb|EV280003.1|EV280003
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298186013|gb|HO031174.1|HO031174
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|19348506|gb|BM893038.1|BM893038
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|38192921|gb|CF922127.1|CF922127
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|213607061|gb|DB965059.1|DB965059
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|192332966|gb|FK024615.1|FK024615
EST:     TTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|8670053|gb|BE191160.1|BE191160
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|14990780|gb|BI316453.1|BI316453
EST:     TTATCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298178097|gb|HO027480.1|HO027480
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298166245|gb|HO009216.1|HO009216
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|213601798|gb|DB982523.1|DB982523
EST:     GGCCTTCTGCTCAG                         AGGCAATGTAGACAAGAAGGAAGTATTAGAGAACTTGGATCTCATTCTAAT
genomic: GGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|38192996|gb|CF922202.1|CF922202
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298179376|gb|HO027847.1|HO027847
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTGTT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298182838|gb|HO031573.1|HO031573
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|14990797|gb|BI316470.1|BI316470
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|151406134|gb|EV275949.1|EV275949
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTT
EST: gi|192321195|gb|FK014285.1|FK014285
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAATTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|120532300|gb|EH260433.1|EH260433
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298170470|gb|HO019094.1|HO019094
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
EST: gi|298166774|gb|HO010213.1|HO010213
EST:     TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAG                         AGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT
genomic: TTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtct ... tcccctctagAGGCAATGTGGACAAGAAGGAAGCACTAGAGAACTTGGATCTCATTCTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATCTTCACTTCTTTGTTACCGGTGGTGATTATGAAAATGAGCTTATCTTAGCCACAGTTCTGCAGGCATTTTTTGATTCTGTGGGCCTTCTGCTCAGgttgtggtcttacataaacaatttatatatgttccatgttcaagggtgtttttaatctatcactattaacacagtagtccttgatgattttactgtcttttcccctctag

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