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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctagcttgtttttcagaaattggattggattttaaactacatactcatagcaattgcttgatgctgatctgcacactaattgtttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA

Basic information

species Glycine max
transcript GLYMA12G04220.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 3
atctagcttgtttttcagaaattggattggattttaaactacatactcatagcaattgcttgatgctgatctgcacact-aattgtttctaatgtgact--agGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA
              | || |||  ||   || |||  ||  | ||  | |    ||      || ||  |||    ||| ||||  |  | ||   | |  |||||| ||||| ||||| ||| ||||||||||||| ||||| ||||||||  | ||||||||| |||||| |||   
-------------gtaagtaataagaagagacttttcacatcttaacctttcagatga---aattcttttcttttaacttaattactcttcattcaattttagGTGGTACAAAAGAGTATAAACTTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTCTGAAACTTGAAAAAGG

upper sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 3
atctagcttgtttttcagaaattggattggattttaaacta-catactcatagcaattgcttgatgctgatctgcacactaattgtttctaatgtgact--agGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA
            | | |  | |    |   || || | ||  || | ||  |  |||   |   ||   | |||   || |||| || ||  |   |||  |||||| || |||||||||||  ||||||||||||| ||||| ||||||||  | |||||| ||||||||| |||   
-------gcaagtctgaagagtctcttaacatcttcatctttcacattc-cattaatctttgactgtctaactg---acaaatt-ttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG

upper sequence: GLYMA12G04220.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 3
atctagcttgtttttcagaaattggattggattttaaactacatactcata-----gcaattgcttgatgctgatctgcacactaattgt------ttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA
           ||   | | |||    | || |  |   || ||| | ||       ||  |     ||  |  | ||| | ||||| ||      ||||  | ||   |||||| |||||||| ||||| ||||| |||||||| || |||||||||||||||||||||||||| |||| ||    
-----------ttgcaaaatatttctgtagagtacatggtatatatttatgtgttgacatgtatacaattttagtttgctccctaatcgtgcctctttcttttctgttaagGTGGTACAAAGGACTACAAGGTTCTCATGGACCAATTCCATCATGTTTCAACTGCTTTTCTGGAGCTTGAAAGAGG

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|209726826|gb|BW672513.1|BW672513
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGAC
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgtgt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGAC
EST: gi|151410377|gb|EV280192.1|EV280192
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgtgt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|15284765|gb|BI468656.1|BI468656
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAAGAGTACAAAGTTCTAATGGAACAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgtgt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatagcaattgcttgatgctgatctgcacactaattgtttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA
                                        ttctaat  putative branch site (score: 2)
                                 taattgtttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctagcttgtttttcagaaattggattggattttaaactacatactcatagcaattgcttgatgctgatctgcacactaattgtttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA