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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatttcttctcattcaccatcctgtaaaaatattagaagattagaatgacaatatgtttctgtttaatgtcatgttaaagtatttgaatgaactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG

Basic information

species Glycine max
transcript GLYMA08G13680.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------gtatgtaatttctt-ctcattcaccatcctg--taaaaatattagaagattagaatgacaata-tgtttctgttta-atgt-catgttaaagtatttgaatgaactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
                |||  ||  | |  |  ||   |     |   |||| |||| |    | |  | |  || || | | |||||||| |  |  ||| | | |  ||  | |      ||  ||  ||||  |||||||||| || || ||||| ||||||||||||||||| |||||||| ||
gtataatgttaccttctataaaaactttgacagatgtgcttgtttacttaaatatatcatgttactgaacttccactaatctatctgtttatacatgtatgatgatgcgttctatt---tccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgtaatttcttctcattcaccatcctgtaaaaatattagaagattagaatgacaatatgtttctgtttaatgtca--tgttaaagtatttgaatgaactgttca--ttgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
                                   ||| ||    | |    || | ||||  |  |  | ||  ||   || | || ||| ||| |  | |  |    ||  ||    |||| ||||| || |||||||||||||||||||||||||| ||||| |||||
---------------------------------gtatagtatgctagtttgctgtccatatcatattactgaacttccattgatcaattatatgattctatttcttgggttcctcggttagGTCATTCCATTTGACAATAAAGGACAGCTCAAGGAAGCCTTTAACATAAG

upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G05420.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtaatttcttctcattcaccatcctgtaaaaatattagaagattagaatgacaata-tgtttctgttta-atgt-catgttaaagtatttgaatgaactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
            | ||  || ||       |||| |||| |    | |  | |  || || | | |||||||| |  |  ||| | | |  ||  | |      ||  ||  ||||  |||||||||| || || ||||| ||||||||||||||||| |||||||| ||
-----------gtgcttgtttact------taaatatatcatgttactgaacttccactaatctatctgtttatacatgtatgatgatgcgttctatt---tccttggtttttcttttagGTTATTCCATTTGATAATAAGGGACAGCTCAAGGAAGCTTTTAATATCAG

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|213615293|gb|DB963487.1|DB963487
EST:     ATCCTGATTGTAGGTTGATTGGACTCCACTTGTATGATGGTTTGTTTAAA                         GTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
genomic: ATCCTGATTGTAGGTTGATTGGACTCCACTTGTATGATGGTTTGTTTAAAgtatgtaatt ... gatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
EST: gi|207808214|gb|GD779039.1|GD779039
EST:     ATCCTGATTGTAGGTTGATTGGACTCCACTTGTATGATGGTTTGTTTAAA                         GTTATTCCCTTCGACAATAGAGGACAGCTCAAGGAAGCATTTAATATAAG
genomic: ATCCTGATTGTAGGTTGATTGGACTCCACTTGTATGATGGTTTGTTTAAAgtatgtaatt ... gatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
EST: gi|209717579|gb|BW679686.1|BW679686
EST:     ATCCTGATTGTAGGTTGATTGGACTCCACTTGTATGATGGTTTGTTTAAA                         GTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
genomic: ATCCTGATTGTAGGTTGATTGGACTCCACTTGTATGATGGTTTGTTTAAAgtatgtaatt ... gatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtttaatgtcatgttaaagtatttgaatgaactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG
                                         cattgat  putative branch site (score: 4)
                                               tcttcc  CT-rich tract
                  ttaaagtatttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatttcttctcattcaccatcctgtaaaaatattagaagattagaatgacaatatgtttctgtttaatgtcatgttaaagtatttgaatgaactgttcattgatcttccagGTTATTCCCTTCGACAATAAAGGACAGCTCAAGGAAGCATTTAATATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA