Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttcctcttctctctcacacactctctctttcatagggtttcagttttttttttctcttcgcttatgcgtctcgttttggttattgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATTTTGAGAACTCCGAAGATGAAAGAAGAACGAGAATTGGATCTCTGAAGAA

Basic information

species Glycine max
transcript GLYMA11G12260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G39170.2 (Arabidopsis thaliana), 3'ss of exon 1
gtaacttcctcttctctctcacacactctctc------tttcatag-ggtttcagttttttttttctcttcgctt-atgcgtctcgttttggttattgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATTTTGAGAACTCCGAAGATGAAAGAAGAACGAGAATTGGATCTCTGAAGAA
 ||   |  |  | | |   |  | |  | |       ||   | | | |||||| |     |   ||   | || |||      |||||  || || |   |||||| || ||| | |   | ||||||||||| |||||||| |  ||||||||||||||||| |||||||| || ||||| ||||| || ||| |||||||
-tagggttgtgctatttacaagcctcaattttgagaagttgggtcgtgatttcagctgccaatagttcagtggttgatgaaaaatgttttcttttttat---agGTTTTGAGGGAATATTGAGCAGTGATGAGAAAAAGGAAAGAAAGTCTGATTTTGAGAACTCAGAAGATGAGAGGAGAACAAGAATCGGTTCTTTGAAGAA

upper sequence: GLYMA11G12260.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 3'ss of exon 2
---gtaacttcctcttctctctcacacactctctc--tttcatagggtttc--agttttttttttctcttcgcttatgcgtctcgttttggttattgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATTTTGAGAACTCCGAAGATGAAAGAAGAACGAGAATTGGATCTCTGAAGAA
    |||  |  | |  |   | || |     |    | | |||   ||    | |  || |  | | |    |  ||  |    ||| |  |||   | |||| || || |||||||| ||   ||||||||  |  ||||| |  ||||||||||| ||||| ||||| ||||| || || |||||||| |||||||| ||
cttataaacttgtgtcattaattacgcgagtacaaaatgttataaatttgtgtaatgcttgtaatttatcaattcttgactaatatttcgactat---gacagGCTTTGAGGGATTCTCTGGTCATGATGAGAGAAGAGAAAGAAAGTCTGATTTTGAAAACTCGGAAGACGAAAGGAGGACAAGAATTGGGTCTCTGAAAAA
















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|213593977|gb|DB961921.1|DB961921
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|193418447|gb|FK384771.1|FK384771
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTACCGGGAGTGATGA
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCT-CCGGGAGTGATGA
EST: gi|213588301|gb|DB967787.1|DB967787
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|209713242|gb|BW681781.1|BW681781
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCAGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|8283332|gb|BE020893.1|BE020893
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|213590510|gb|DB968088.1|DB968088
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCAGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|213603344|gb|DB966603.1|DB966603
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|209719529|gb|BW651007.1|BW651007
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCACTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|298171644|gb|HO021236.1|HO021236
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
EST: gi|208046631|gb|GD849131.1|GD849131
EST:     GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCT                         GTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT
genomic: GACCCTTGAAACCACAATGTCCGGCCCGCTCGACCGCTTCGCTAGACCCTgtaacttcct ... attgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcagttttttttttctcttcgcttatgcgtctcgttttggttattgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATTTTGAGAACTCCGAAGATGAAAGAAGAACGAGAATTGGATCTCTGAAGAA
       ttttttttttctctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttcctcttctctctcacacactctctctttcatagggtttcagttttttttttctcttcgcttatgcgtctcgttttggttattgtggcagGTTTCGAAGGATTCTCCGGGAGTGATGAGAAGAAGGAAAGGAGATCTGATTTTGAGAACTCCGAAGATGAAAGAAGAACGAGAATTGGATCTCTGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA