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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctttattactgcagcatgttttatatcttaacattgtgaaatgctttgataaaatgttagcaactgttaagtgaaaatgttcctctttttgtaatacagAATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATACATCTTATGTGAATGATGCAATTTTTACAAATGATGGGAGTCGTGTTATT

Basic information

species Glycine max
transcript GLYMA08G13560.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 10
gctttattactgcagcatgtt-ttatatcttaacattgtgaaatgctttgataaaatgt--tagcaactgttaagtgaaaatgttcctctttttgtaatacagAATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATACATCTTATGTGAATGATGCAATTTTTACAAATGATGGGAGTCGTGTTATT
  |||     | ||    ||  |||| |      ||||  | |   | |  |  ||| |  || ||| |  | | |  | || ||   |||| | | || |||||| |||||  | |||||||| ||  |||||||||| || ||||| || ||||||||||| ||| |||| || ||||||| |||||| || ||| |||| 
-attttccttttcatttggtagttatgtaagtttattggtagagcttctagtcgaatataatatcaaattcttatt--atatattttgctttattttatgcagAATCCATGGTTTGAAATCTGGGAAATTGTTGAAAGAATTTCGTGGTCACACATCTTATGTAAATCATGCCATCTTTACAAGTGATGGAAGCCGTATTATC

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 10
---------gctttattactgcagcatgttttatatcttaacattgtgaaatgctttgataaaatgttagcaactgttaagtgaaaatgttcctctttttgtaatacagAATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATACATCTTATGTGAATGATGCAATTTTTACAAATGATGGGAGTCGTGTTATT
         | ||||| | |   | ||||| |  ||  | | || |   |   |     |    ||||  ||| |||||  |    |  ||   || | | | ||  ||||| ||||| || || ||||| ||  |||| || || |||||||||||| ||||||||||||||||||| || ||||||||||| ||  |||||||| ||
tgtgaggcagttttatcaattttg-atgttattgattatgaaataggagaggacccc--ttggttgtt--caaatgttactt----accttatgctatgtttgatttagAATCCATGGACTGAAGTCTGGGAAACTGTTAAAGGAATTCCGTGGCCATTCATCTTATGTGAATGATGCTATATTTACAAATGACGGAGGTCGTGTTGTT
















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|193453833|gb|FK421170.1|FK421170
EST:     TCTCGTGATGGAAGCCAGTTATTAAGCACTTCATTTGACAGCACAGCAAG                         AATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATAC
genomic: TCTCGTGATGGAAGCCAGTTATTAAGCACTTCATTTGACAGCACAGCAAGgttttcattt ... tgtaatacagAATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATAC
EST: gi|192300449|gb|FG987906.1|FG987906
EST:     TCTCGTGATGGAAGCCAGTTATTAAGCACTTCATTTGACAGCACAGCAAG                         AATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATAC
genomic: TCTCGTGATGGAAGCCAGTTATTAAGCACTTCATTTGACAGCACAGCAAGgttttcattt ... tgtaatacagAATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgataaaatgttagcaactgttaagtgaaaatgttcctctttttgtaatacagAATTCATGGCCTCAAATCTGGAAAGATGTTGAAAGAGTTCCGTGGCCATACATCTTATGTGAATGATGCAATTTTTACAAATGATGGGAGTCGTGTTATT
 ctttgat  putative branch site (score: 5)
                                 tgttcctctttttgt  putative PPT
                                         tttttgtaata  TA-rich tract