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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgataatttctttgaaagtgtaaattgtaaaaaaaaaattacatgtgtcacactcaaactctttaaggttgtttatttcaatgggtgactgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGGTGAAAGTGTTTGATTTGAATGGAAACGGGATTCCAATTTCTGACTTGTG

Basic information

species Glycine max
transcript GLYMA19G36130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36130.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g03130.t01 (Vitis vinifera), 3'ss of exon 1
tatgataatttctttgaaagtgtaaattgtaaaaaaaaaattacatgtgtcacactcaaact--ctttaaggttgtttat--ttcaatgggtgactgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGGTGAAAGTGTTTGATTTGAATGGAAACGGGATTCCAATTTCTGACTTGTG
   | ||| ||   ||  | |  | |  |||||  | |       |  |  | ||   ||||   || ||||   || ||  || || | || | ||  | ||||| |||| ||| |     |  |||| ||||||||||  | | |||||   | | |||||||||||||||||||||||||||||||||||||||| |||||
---gttaaattaaatgctattagagag-gtaaattacatccagtcttcggaagacgtgaactggtttgaaggcacttgataattgaacgtgttaatgtaaccagGAATTGAATCTTCCACTGTTAGTGATGATACCACGAACTTATTGGATAGAGCGCAAGTGTTTGATTTGAATGGAAACGGGATTCCAATTTCTGATTTGTG
















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|4305601|gb|AI443785.1|AI443785
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|9258245|gb|BE346392.1|BE346392
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|151403056|gb|EV272866.1|EV272866
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|9258744|gb|BE346891.1|BE346891
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|192297273|gb|FG990621.1|FG990621
EST:     AACAATTCAATACCACGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|15287410|gb|BI471301.1|BI471301
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|15202597|gb|BI425484.1|BI425484
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|15284825|gb|BI468716.1|BI468716
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAT                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|120496088|gb|EH224255.1|EH224255
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|27425152|gb|CA936672.1|CA936672
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
EST: gi|27809251|gb|CB063673.1|CB063673
EST:     AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAG                         GAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG
genomic: AACAATTCAATACCATGCAACAACCACACCCTTTGTTGCTGCTTCTGCAGgcaagtcttg ... ctgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtcacactcaaactctttaaggttgtttatttcaatgggtgactgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGGTGAAAGTGTTTGATTTGAATGGAAACGGGATTCCAATTTCTGACTTGTG
                         ttgtttatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgataatttctttgaaagtgtaaattgtaaaaaaaaaattacatgtgtcacactcaaactctttaaggttgtttatttcaatgggtgactgagaacagGAGTTGAGTCTCCGGTGTTGGGTGAGGATACCACGAGTTCACTGGATTCGGTGAAAGTGTTTGATTTGAATGGAAACGGGATTCCAATTTCTGACTTGTG

- - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - cacactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgggtga