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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctcaatctttttagtagtgttattattgccctatgttttattgtgacactttcaagatatattagcccagcttggacttgcatttgggacttc...

Basic information

species Glycine max
transcript GLYMA05G22320.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 9
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 9
GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctcaatctttttagtagtgttattattgccctatgttttattgtgacactttcaagatatattagcccagcttggacttgcatttgggacttc
|||||||| ||||| ||||||||  |  | ||||||||||||||| | || ||||| |||||||| ||||||||     | | || ||     | ||  ||  |   | | | ||||  | |||  |    ||||    ||   |   |||| ||  |           
GCTGTTGATTTTGTGGACAAGTTGCTGAGATATGATCACCAAGAAAGGCCAACAGCTAAAGAAGCAATGgtaagcaacaatttttctttaatatctttctaaagattt-tctcttataattacagataagtgatagtagagaatatgatggatttttacag--------

upper sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 9
GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctcaatctttttagtagtgttattattgccctatgttttattgtgacactttcaagatatattagcccagcttggacttgcatttgggacttc----
 |  |||||||| ||||||||||  | || ||||||||||||||| | || || ||||||||||| ||||||| | | |  |  |  |  | |   ||  | ||  |  ||   || ||| |    |     ||  ||||||     ||  ||       | ||| |      
TCAATTGACTTTCTTGACAAGTTGCTGCGATATGATCACCAAGAAAGGCCAACCGCAAAAGAAGCAATGgtaaaacccc--tgatcattattgccctaaaaatgaacgctgaactactgtaaatactctttaatgcattagctt--tttaaaccatttgattggattggaatg
















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|31470201|gb|CD412349.1|CD412349
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|16279966|gb|BI943709.1|BI943709
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|17153984|gb|BM143917.1|BM143917
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|17518848|gb|BM187890.1|BM187890
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|20814462|gb|BQ298940.1|BQ298940
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGT
EST: gi|192303250|gb|FG995586.1|FG995586
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|31465610|gb|CD407638.1|CD407638
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|16343159|gb|BI968754.1|BI968754
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|22927857|gb|BU544996.1|BU544996
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|4299430|gb|AI442903.1|AI442903
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAAT-CAGAAAGTAGTAAAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|7327072|gb|AW620870.1|AW620870
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
EST: gi|17401154|gb|BM177936.1|BM177936
EST:     AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG                         GCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT
genomic: AGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctc ... tgatatgcagGCCCATCCATACTTCAATCCAGTTAGAAATGCAGAAAGTAGTAGAACTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATGgtaagatctcaatctttttagtagtgttattattgccctatgttttattgtgacactttcaagatatattagcccagcttggacttgcatttgggacttc

- - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC