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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtacttcaataaaataattatatagcaaaagagcattcctggttccatttttctgtatttctgattatatatgtgaataatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAATTTAAAGGAGATGGTTATACAATCTGTGCAG

Basic information

species Glycine max
transcript GLYMA20G27000.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 6
gtatttgtacttcaataaaataattatatagcaaaagagcattcctggttccatttttctgtatttctgattatatatgtgaataatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAATTTAAAGGAGATGGTTATACAATCTGTGCAG
                  |||||  | |   ||   |       |  | |  ||| ||   | |  ||  | | |  ||    || || |||||||||| || || |||||||| |||||||||||| |||| ||||||||| | ||||| ||||||||||| |    ||||| ||
----------------gtaataaccaaaattcactgggattacacatgcttaattgtta-atgtgcctattaacagttgcatttatttactcagGATACATTTCGCGGGAGAGTGTGTGAATGCCCCTTGGTTGATGGTGTGAAGTTTAAGGGAGATGGTTACAGTTCCTGTGAAG

upper sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ06539 (Selaginella moellendorffii), 3'ss of exon 5
gtatttgtacttcaataaaataattatatagcaaaagagcattcctggttccatttttctgtatttctgattatatatgtgaataatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAATTTAAAGGAGATGGTTATACAATCTGTGCAG
                                          | ||| |||||  | | || |   |||| |     | |   |  |   ||||||||| ||||| ||  |||| ||||| |||||| ||||| | |||||||| ||| | |||||||||||||    ||| | ||
-------------------------------------gtaggttctgcttccagctctatggaccactgaat---cgtctctgttgtggttcagGATACCTTCCGGGGCCGAGTTTGTGAGTGCCCCGTGGTGCAAGGTGTGCAGTTTGACGGAGATGGTTATAGCCACTGCGAAG
















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|7233271|gb|AW568619.1|AW568619
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTTCGTGGGAGAGTTTGTGAATGCCCCCTGTTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|193362601|gb|FK325355.1|FK325355
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|208340230|gb|GE136996.1|GE136996
EST:     CACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: CACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|16997296|gb|BM086668.1|BM086668
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|193547843|gb|FK505124.1|FK505124
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|193445332|gb|FK409385.1|FK409385
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|37994040|gb|CF805786.1|CF805786
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGA
EST: gi|193348579|gb|FK317711.1|FK317711
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACTTTCCGTGGGAGAGTA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTA
EST: gi|151400595|gb|EV270409.1|EV270409
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|151407733|gb|EV277548.1|EV277548
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|298171587|gb|HO021179.1|HO021179
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|208186785|gb|GD983527.1|GD983527
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|15286008|gb|BI469899.1|BI469899
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|192304755|gb|FG994991.1|FG994991
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|193314337|gb|FK280138.1|FK280138
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
EST: gi|193696330|gb|FK640178.1|FK640178
EST:     ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAAT
genomic: ATAATGGTGGTTGTTGGCAGGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAAT
EST: gi|298197470|gb|HO044949.1|HO044949
EST:     GGATAAAGTAGCTAACATCACCGCATGCAAG                         GATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA
genomic: GGATAAAGTAGCTAACATCACCGCATGCAAGgtatttgtac ... aatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcctggttccatttttctgtatttctgattatatatgtgaataatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAATTTAAAGGAGATGGTTATACAATCTGTGCAG
                         ttctgat  putative branch site (score: 3)
                                               tttctc  putative PPT
                      tatttctgattatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtacttcaataaaataattatatagcaaaagagcattcctggttccatttttctgtatttctgattatatatgtgaataatttctcagGATACGTTCCGTGGGAGAGTATGTGAATGCCCCCTGGTGGATGGTGTGCAATTTAAAGGAGATGGTTATACAATCTGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG