Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatccttcataatgcctatattctgatgtcattttatggactaccttctactaagaatgtggacttttgggatataacataagggctgtgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGATGACCTGCACTTGGTAGAGCATGTGCTGGATTCAGCTGCACAGGAGTATG

Basic information

species Glycine max
transcript GLYMA08G02420.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G02420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g01000.t01 (Vitis vinifera), 3'ss of exon 3
tcaatccttcataatgcctatattctgatgtcattttatggactaccttctactaagaatgtggacttttgggatataacataagggc-------tgtgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGATGACCTGCACTTGGTAGAGCATGTGCTGGATTCAGCTGCACAGGAGTATG
      ||   | ||| | |  || ||   | || |     | ||  |  |  |    |||||  | ||||  |||  || || | |        | |||||| ||| |||| || ||| |||| |||||| ||||||||||| | ||||||||||||||| |||| ||||| ||   | |  ||||||| ||     | |||||||
-----tctaattcatgac-aagttttggcatgatatataaaaatatttagtcattgtcatgtgt-cctttgatatagtacttatgagtgtaacaatatgtgttgcagAGTTTACTCAGATTGAAGGAACCTGCTGTCTTATTGCGTTGTCGGAAAGATGACTTGCATTTGGTGGAATCTATCTTGGATTCCGCAAAGGATGAGTATG

upper sequence: GLYMA08G02420.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g00960.t01 (Vitis vinifera), 3'ss of exon 1
tcaatccttcataatgcctatattctgatgtcattttatggactaccttctactaagaatgtg-gacttttgggatataacataagggc-------tgtgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGATGACCTGCACTTGGTAGAGCATGTGCTGGATTCAGCTGCACAGGAGTATG
       ||||||  ||   | ||   ||| |||       |  |  ||     |      || | | ||||  |||  || ||   |        | |||||  |||  ||| || ||| |||| |||||| ||||||||||| | ||||||||||||||| |||| ||||| ||   | |  ||||||||||     | |||||||
------attcata--gcaagttttggcatgacataaggataaaaatatttagtcattgtcttgtgtcctttgatatagtacgtataagtctaacaatatgtgtcgcagAATTTACTCAGATTGAAGGAACCTGCTGTCTTATTGCGTTGTCGGAAAGATGACTTGCATTTGGTGGAATTTATCTTGGATTCAGCAAAGAATGAGTATG
















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|207749360|gb|GD719574.1|GD719574
EST:     CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
genomic: CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
EST: gi|15663576|gb|BI700947.1|BI700947
EST:     CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
genomic: CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
EST: gi|13252165|gb|BG363068.1|BG363068
EST:     CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
genomic: CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
EST: gi|6455236|gb|AW185919.1|AW185919
EST:     CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
genomic: CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
EST: gi|193451550|gb|FK420630.1|FK420630
EST:     CTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
genomic: CTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
EST: gi|7639786|gb|AW734101.1|AW734101
EST:     CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCNGAAAGAT
genomic: CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
EST: gi|193377800|gb|FK343256.1|FK343256
EST:     CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAG                         TGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT
genomic: CTCATCATGATCATGTGTACAGAAACCTTCTGAAAGATCTCATTATTCAGgtcagttgaa ... tgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttctactaagaatgtggacttttgggatataacataagggctgtgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGATGACCTGCACTTGGTAGAGCATGTGCTGGATTCAGCTGCACAGGAGTATG
                            atataac  putative branch site (score: 3)
                            atataacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatccttcataatgcctatattctgatgtcattttatggactaccttctactaagaatgtggacttttgggatataacataagggctgtgtgttacagTGTTTGCTTAGACTGAAAGAACCTTCTGTCTTATTGAGATGTCGGAAAGATGACCTGCACTTGGTAGAGCATGTGCTGGATTCAGCTGCACAGGAGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - tccttca
- - - - - - aatgcct
- - - - - - - - - - - - -tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttttgg