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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCTTAACATCACCGATGACACTAGAGTCCGTGCTGCTGTTCCCACCATCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctttataaaccattttatttttaatgtggtttttaggtatctgggtgtgttttgtttaagtctaggaatgatttggaatctgggtttgtgttt...

Basic information

species Glycine max
transcript GLYMA08G17600.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 1
CAACCTTAACATCACCGATGACACTAGAGTCCGTGCTGCTGTTCCCACCATCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctttataaaccattttatttttaatgtggtttttaggtatctgggtgtgttttgtttaagtctaggaatgatttgga-atctgggtttgtgttt-
 |||  |||||||||||||||||| ||  | ||||| ||||||||||||||||||||||| |  ||| ||||| | |  ||  | || |  || ||||||||||| | | | ||   || ||     || |     |  |||  | | ||    | |  |||   | | | |   |||| ||   ||| ||       |   
TAACTCTAACATCACCGATGACACCAGGATTCGTGCCGCTGTTCCCACCATCAAGTACTTGATGGGTAATGGATCTAGGGTTGTTCTCTGCAGTCACTTGgtatgatatct-tatctcagttctcacttcactacttgcttatctgt-tgtaattttggtgtgggaattttgatctgatctgtttatccggagagccatgcg

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 5'ss of exon 1
CAACCTTAACATCACCGATGACACTAGAGTCCGTGCTGCTGTTCCCACCATCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctttataaaccattttatttttaatgtggtttttaggt-atctgggtgtgttttgtttaagtctaggaat--gatttggaatctgggtttgtgttt
 |  || || |||||||||||||| ||||||||||| ||||| ||||||||||||||||| |  |||||||| || ||||| |||||  | |||||| | ||||| ||   ||   |  ||   | |||  | |  || ||   | |||||||| | || | |||  |   |    |  | |||    ||||| |   |    
GAGTCTCAAGATCACCGATGACACCAGAGTCCGTGCCGCTGTGCCCACCATCAAGTACTTGATGGGTCATGGCGCTAAAGTCATCCTCGCCAGCCACCTTgtatgatccggatttccatttacttctttgttttccttgttttatgatctgggtcttttgttttttgggaaaacgttttgtttttttgtctggatcaata---
















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|209709349|gb|BW678893.1|BW678893
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|209714549|gb|BW662212.1|BW662212
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|298198247|gb|HO039786.1|HO039786
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|213590565|gb|DB968115.1|DB968115
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|24206138|gb|BU965391.1|BU965391
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|213610576|gb|DB960615.1|DB960615
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|213590392|gb|DB971540.1|DB971540
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|5606888|gb|AI900986.1|AI900986
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|8402320|gb|BE057954.1|BE057954
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|213589598|gb|DB965814.1|DB965814
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|298165436|gb|HO011485.1|HO011485
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCATTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTTTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|151412432|gb|EV282244.1|EV282244
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|192295471|gb|FG987085.1|FG987085
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|213608836|gb|DB957200.1|DB957200
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|213610262|gb|DB962932.1|DB962932
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|8402319|gb|BE057953.1|BE057953
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACA-TTTGAAGCCTCT
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCT
EST: gi|209721583|gb|BW671724.1|BW671724
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|21600463|gb|BQ610794.1|BQ610794
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|16347493|gb|BI973088.1|BI973088
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|254341877|gb|GR853014.1|GR853014
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|298188541|gb|HO035234.1|HO035234
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
EST: gi|15661932|gb|BI699303.1|BI699303
EST:     TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTG                         GGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA
genomic: TCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctt ... ctgttttcagGGACGTCCTAAAGGTGTAACACCTAAATACAGTTTGAAGCCTCTTGTGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCTTAACATCACCGATGACACTAGAGTCCGTGCTGCTGTTCCCACCATCAAGTACTTAACTGGTCATGGAGCCAAAGTGATCCTTTCTAGCCACTTGgtatgttctttataaaccattttatttttaatgtggtttttaggtatctgggtgtgttttgtttaagtctaggaatgatttggaatctgggtttgtgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA