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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttcgtccattttcatgtttttttttttcgttctttcatgctgcagtcttttaagcatttgatttgatttttaaataaattgctgagcttttccacagCTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCATGTCTGGATTTAGTTGTGGCAAATGCATGTTCAGAATTTGTTACAAG

Basic information

species Glycine max
transcript GLYMA20G39210.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39210.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G05790.1 (Arabidopsis thaliana), 3'ss of exon 10
cttttcgtccattttcatgtttttttttttcgttctttcatgctgcagtcttttaagcatttgatttgatttttaaataaattgctgagcttttccacagCTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCATGTCTGGATTTAGTTGTGGCAAATGCATGTTCAGAATTTGTTACAAG
             | | | |||  ||  |      || |||||     | | || | ||| |  |||  ||| | | |   || ||    ||      |||||  |  | | | |||||| ||  |||| ||  | ||||| || ||||||||| | ||||  | ||||||| | |||||||||||||||||||||||
------------gtacgtttttaattaataaaaggttacatgcc----tttctttaacatatc-tttcgtttctgagttcttttctt--tttgcgggtagCTTCGTTGCAGATTCCCTAACCTATATGTATATGCCTATGGACCTCTCCCATGTGTAGATTCGGATGTGGCAGAGGCATGTTCAGAATTTGTTACAAG

upper sequence: GLYMA20G39210.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0124g00200.t01 (Vitis vinifera), 3'ss of exon 4
-cttttcgtccattttc-atgtttttttttttcgttctttcatgctgcagtcttttaagcatttgatttgatttttaaataaattgctgagcttttcca--cagCTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCATGTCTGGATTTAGTTGTGGCAAATGCATGTTCAGAATTTGTTACAAG
   |   ||| |  ||  ||| | |||||  |  ||||||  || |    |||||||    ||||   ||||    |   ||    ||   |||||     ||| | |||  ||| ||||| ||| | ||||| || || |||||| | || |||||| |||||| |||||| ||| ||||||||||||||||||| |||||
aaatgctgtcaagattggatgctatttttcatttttcttt--tgtttttttctttta--tttttgtcatgatgaaaatgcaatgcccttttctttttttgtcagTTGTATGGCCGATACCCAAATTTACATGTCTATTCCTATGGGACCCTTCCATGTGTGGATTCAGTTGTAGCAGATGCATGTTCAGAATTTGTCACAAG
















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|15813881|gb|BI786156.1|BI786156
EST:     TAGTTGGGCATTCACTTGGGGGTGCTATAGCTGCATTGCTTGGACTGCAA                         CTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCA
genomic: TAGTTGGGCATTCACTTGGGGGTGCTATAGCTGCATTGCTTGGACTGCAAgtatgacatt ... ttttccacagCTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCA
EST: gi|21888693|gb|BQ741906.1|BQ741906
EST:     TAGTTGGGCATTCACTTGGGGGTGCTATAGCTGCATTGCTTGGACTGCAA                         CTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCA
genomic: TAGTTGGGCATTCACTTGGGGGTGCTATAGCTGCATTGCTTGGACTGCAAgtatgacatt ... ttttccacagCTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtcttttaagcatttgatttgatttttaaataaattgctgagcttttccacagCTTTATAACCGCTACCCTAATCTGCATGTTTACTCATATGGGCCACTCCCATGTCTGGATTTAGTTGTGGCAAATGCATGTTCAGAATTTGTTACAAG
                  atttgat  putative branch site (score: 5)
                                            cttttccac  putative PPT
     ttttaagcatttgatt  TA-rich tract