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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgcatataattttttttgtgtgcgtgccagtgtttcaaagttagactattaaagcgagctttcaaatttgtttaattactatgtgttacttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAACTGGGATGAACCAACCACTAA

Basic information

species Glycine max
transcript GLYMA08G19430.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19430.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S1_300V6.2 (Physcomitrella patens), 3'ss of exon 7
cattgcatataattttttttgtgtgcgtgccagtgtttcaaagttagactattaaag-cgagctttcaaatttgtttaattactatgtgttacttgcat----agATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAACTGGGATGAACCAACCACTAA-----------------------------
     ||  |  |||||  ||  |  || |  ||       |||| |  ||| |    | | | ||   |  |||| |  |  |   |  || |||| |    |||| || |  || || |||||||| || ||||||||||||||||||| | ||||||| |  || || || ||                             
----acacttggtttttgatg-atttgttcttgtaaagtccagttggcttatgaccttccatcatttgcaactgttaatctgatcgtttctatttgcttcgtcagATTCCCAAAAAGGGCAAGATTTACTCTGTGAATGAAGGAAATGCCAAACACTGGGACGGGCCCACAACGAAGTATGTGGAGAACGCCAAGTTTCCCAAGG

upper sequence: GLYMA08G19430.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ23220 (Selaginella moellendorffii), 3'ss of exon 7
cattgcatataattttttttgtgtgcgtgccagtgtttcaaagttagactattaaagcgagctttcaaatttgtttaattactatgtgttacttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAACTGGGATGAACCAACCACTAA-----------------------------
                                                      ||| ||| |||  |  || |  | |    |  |  |   |  |||| | ||||| || |||||||||||||| ||||| ||||||||||| |   |||||||||||||||| |  ||                             
----------------------------------------------------gtaagtgagttttatatgttttgcagtgttaacttaatgtct-tatagGTTCCAAGGAAGGGAAAGATTTATTCTGTGAACGAAGGAAATGCTAAGCACTGGGATGAACCAACAAAAAAATACGTGGAGATTGCAAAGTTTCCGACAG

upper sequence: GLYMA08G19430.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ25223 (Selaginella moellendorffii), 3'ss of exon 7
cattgcatataattttttttgtgtgcgtgccagtgtttcaaagttagactattaaagcgagctttcaaatttgtttaattactatgtgttacttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAACTGGGATGAACCAACCACTAA-----------------------------
                                                      | | ||| |||  |  || |  | |    |  |  |   |  |||| | ||||| || |||||||||||||| ||||| ||||||||||| |   ||||||| |||||||| |  ||                             
----------------------------------------------------gtacgtgagttttatatgttctgcagtgttaacttaatgtct-tatagGTTCCAAGGAAGGGAAAGATTTATTCTGTGAACGAAGGAAATGCTAAGCACTGGGACGAACCAACAAAAAAATACGTGGAGATTGCAAAGTTTCCGACGG

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|22927213|gb|BU544352.1|BU544352
EST:     CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|254339115|gb|GR847832.1|GR847832
EST:     CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|163921427|gb|EH038965.1|EH038965
EST:     CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|208151927|gb|GD945630.1|GD945630
EST:     CCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|21888792|gb|BQ742005.1|BQ742005
EST:     CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|193310611|gb|FK276775.1|FK276775
EST:     CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|254339114|gb|GR847831.1|GR847831
EST:     CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CACTTGATCCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|208200102|gb|GD996031.1|GD996031
EST:     CCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|193333960|gb|FK301348.1|FK301348
EST:     CCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
EST: gi|208170359|gb|GD968404.1|GD968404
EST:     CCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAG                         ATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC
genomic: CCTAGCCTTGGGGAGTTCATATTGACTCACCCAAACATCAAGgtacataaaa ... acttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactattaaagcgagctttcaaatttgtttaattactatgtgttacttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAACTGGGATGAACCAACCACTAA
                           gtttaat  putative branch site (score: 4)
                 tttcaaatttgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgcatataattttttttgtgtgcgtgccagtgtttcaaagttagactattaaagcgagctttcaaatttgtttaattactatgtgttacttgcatagATACCAAGTAAAGGAAAGATTTATTCGGTGAATGAAGGAAATGCCAGAAACTGGGATGAACCAACCACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -tgcatat
- - - - - - - - ttttgtg
- - - - - - - - - - - - gcgtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtg