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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctgtatgcagctattttacctttatttttcttatctctttcattaaaattatatgttaagttactcttttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT

Basic information

species Glycine max
transcript GLYMA11G16220.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G16220.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0220g00070.t01 (Vitis vinifera), 3'ss of exon 4
gtatgatctgtatgcagctattttacctttatttttcttatctctttcattaaaattatatgttaagttactcttttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT
         ||||| || |  ||||  |||  ||| | | |   |   |   |  |||  | || ||  ||| |  ||   |||||||  | |||||||||||||| ||||| |||||||| || ||  ||||||||||||| |||||||| ||||||||| | || ||  |
---------gtatgaagtt--tttatatttgatttccctctacatgcaac--aggttacttattcagaaactttgctcctgcagGTATTGAGCCTTATGTAACTTTATACCACTGGGATCTCCCTCTATATCTTCACGAGTCAATGGGAGGGTGGTTAAATGAGCAGATTGT
















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|298170350|gb|HO018974.1|HO018974
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|151395074|gb|EV264945.1|EV264945
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|151393509|gb|EV263384.1|EV263384
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|193692225|gb|FK631096.1|FK631096
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|192300022|gb|FG991840.1|FG991840
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|298189266|gb|HO037669.1|HO037669
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|254323234|gb|GR840039.1|GR840039
EST:     ATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: ATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|298196849|gb|HO041592.1|HO041592
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|192296626|gb|FG991194.1|FG991194
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|298177939|gb|HO023788.1|HO023788
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|26268409|gb|CA819472.1|CA819472
EST:     TTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: TTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|151396070|gb|EV265947.1|EV265947
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAAC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAAC
EST: gi|192314382|gb|FK008058.1|FK008058
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
EST: gi|192314383|gb|FK008059.1|FK008059
EST:     CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAG                         GTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC
genomic: CGAAGGGATAACTTTTTATAACAACATTATTAATGGTCTTCTTGAAAGAGgtatgatctg ... tttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttcttatctctttcattaaaattatatgttaagttactcttttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT
                                      ttactcttttct  CT-rich tract
        ttatctctttcattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatctgtatgcagctattttacctttatttttcttatctctttcattaaaattatatgttaagttactcttttctgacagGTATACAACCTTATGTAACTTTGTACCATTGGGATCTTCCGCTGCATCTTCACGAGTCGATGGGAGGATGGTTAAATAAACAAATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG