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

gtatgtgatctattggagcttttgctttgccccaatacctattttctgaatgtttattcattacatgacattttgtctctatgttgttacatttatttgaatgtgctttctctgatgttctgctattaatgaattgtgattttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG

Basic information

species Glycine max
transcript GLYMA17G01360.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgtgatctattggagcttttgctttgccccaatacctattttctgaatgtttattcattacatgacattttgtctctatgttgttacatttatttgaatgtgctttctctgatgttctgctattaatgaattg----tgattttctttt-tagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
                                                                |    | | |   || ||      |   ||| |   |     |||    ||  |   | ||||||  |||      ||||||    ||  |||||| ||||| |||||||||||||| ||||||||||| |||||||
--------------------------------------------------------------gtacagaaatataaatcaata-----aagcttactaagacacatttt----gaaatctagatattaaaaaatcagagttgatttcaacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG

upper sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 13
gtatgtgatctattggagcttttgctttgccccaatacctattttctgaatgtttattcattacatgacattttgtctctat--gttgttacatttatttgaatgtgctttctctgatgttctgctattaatgaattgtgattttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
                                                       ||| || |   |   | |  ||||  |   | ||| |  |||||| | |       ||    | | |  |  ||  |||||| | |   |  ||  |||||| ||||| ||||||||||||||||||||||| || ||||| |
----------------------------------------------------agcatttatcaggggggttctcatctcagttcatcgtttccattattt-agtacatcagctaacctttccatccctttctgaattctaaaactgcttgcagGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG
















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|193610338|gb|FK566168.1|FK566168
EST:     TGTTGGTGGAACTGCACTTACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|208025739|gb|GD826615.1|GD826615
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|19348946|gb|BM893478.1|BM893478
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAACCC-TGATCAAGAAGGCAATGGTGGAGCTTGAA
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAA
EST: gi|58019435|gb|CX706177.1|CX706177
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|7924124|gb|AW830150.1|AW830150
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|254317928|gb|GR832096.1|GR832096
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|207764437|gb|GD735802.1|GD735802
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|57574880|gb|CX547855.1|CX547855
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|254330862|gb|GR842127.1|GR842127
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|5342423|gb|AI794707.1|AI794707
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
EST: gi|193426110|gb|FK390397.1|FK390397
EST:     TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATG                         GTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
genomic: TGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatc ... ttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaatgtgctttctctgatgttctgctattaatgaattgtgattttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
                           tattaat  putative branch site (score: 2)
                                           ttttcttttt  putative PPT
                           tattaatgaattgtga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgatctattggagcttttgctttgccccaatacctattttctgaatgtttattcattacatgacattttgtctctatgttgttacatttatttgaatgtgctttctctgatgttctgctattaatgaattgtgattttctttttagGTAAATTCAAACCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG