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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacaacctttatcaatcatcaggagaatggttttattgtatatgtgcctcaaaatttattgatgctgatctgcacattaattgtttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA

Basic information

species Glycine max
transcript GLYMA11G11960.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34650.1 (Arabidopsis thaliana), 3'ss of exon 3
agacaacctttatcaatcatcaggagaatggttttattgtatatgtgcctcaaaatttattgatgctgatctgcaca-ttaattgtttctaatgtgact--agGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA
            | | | || || |||   |  || |   || |   |||   |  | |   || ||  |||    | ||||||  |  | ||   | |  |||||| ||||| ||||| ||| ||||||||||||| ||||| ||||||||  | ||||||||| ||||||  ||   
-----------gtaagtaataagaaga---gacttttcacatcttaacctttcagatga--aattcttttcttttaacttaattactcttcattcaattttagGTGGTACAAAAGAGTATAAACTTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTCTGAAACTTGAAAAAGG

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 3
agacaacctttatcaatcatcaggagaatggttttattgtatatgtgcctcaaaatttattgatgctgatctgcacatt----aattgtttctaatgtgact--agGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA
             |||   || | ||| |  | |||   | |   |   ||| | |  ||| ||  |   |||   |      || | || ||  |   |||  |||||| || |||||||||||  ||||||||||||| ||||| ||||||||  | |||||| |||||||||  ||   
------------gcaa--gtctgaagagtc-tcttaacatcttcatctttcacattccattaatctttgactgtctaactgacaaattttacttgttcaactttagGTGGTACGAAGGAGTACAAGATTCTAATGGACCAATTTCACCATGTTTCTGCAGCTTTTTTGGAACTTGAAAAAGG

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 3
agacaacctttatcaatcatcaggagaatggttttattgtatatgtgcctcaaaatttat-tgatgctgatctgcacattaattgt------ttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA
        |  |  |    || | ||| |   |    | ||| | ||  |  | || |||   ||  |  | ||| |  |||| ||      ||||  | ||   |||||| |||||||| ||||| ||||| |||||||| || |||||||||||||||||||||||||| ||||  |    
-------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|193389048|gb|FK354843.1|FK354843
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|14010995|gb|BG725917.1|BG725917
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|10709996|gb|BF009720.1|BF009720
EST:     ACTGATAGCCTTTCACCGTCATATGTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAA
EST: gi|208160470|gb|GD958766.1|GD958766
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTCTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|209722769|gb|BW682867.1|BW682867
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|27446333|gb|CA953456.1|CA953456
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|20813646|gb|BQ298124.1|BQ298124
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|209725283|gb|BW672760.1|BW672760
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|193385511|gb|FK350747.1|FK350747
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|193499460|gb|FK461255.1|FK461255
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|213595316|gb|DB968448.1|DB968448
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
EST: gi|209714966|gb|BW650812.1|BW650812
EST:     ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT                         GTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA
genomic: ACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCATgtgagtgagt ... atgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctcaaaatttattgatgctgatctgcacattaattgtttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA
                                        ttctaat  putative branch site (score: 2)
                               attaattgtttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacaacctttatcaatcatcaggagaatggttttattgtatatgtgcctcaaaatttattgatgctgatctgcacattaattgtttctaatgtgactagGTGGCACAAAGGAGTACAAAGTTCTAATGGACCAGTTTCATCATGTTTCAACTGCTTTTCTGGAACTTGGGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA