Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attactgctataattgatagactagatgtttttgtttctcaagttgtaggtcatgttttccttttgtaacagtatttgtcttcctttaatgtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAATGATCCTGACACACATGATGACTTCAAGCCAGCTAATAAACTTGAGAATT

Basic information

species Glycine max
transcript GLYMA13G44000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44000.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 3'ss of exon 2
attactgctataattgatagactagatgtttttgtttctcaagttgtaggtcatgttttcctttt-gtaacagtatttgtc------ttcctttaatgtcttcacagCTAACTAGGTCCTGTTATCA---TGGAATGAGATACTTTGCTACTGTATCAAATGATCCTGACACACATGATGACTTCAAGCCAGCTAATAAACTTGAGAATT
     ||||  || | ||    ||  |   | |  ||    |    |   | ||| |||| |    || | | |||||||       || | ||||  | ||   || |  || | |||  ||  ||   ||||||||| ||||   |||||||  | ||||||||||||||||||||||| |||||  |  ||||||| ||||| |   
-----tgcttgaagtcatc--ttactttgctctaattggagatgattgcttgatgctttcttcccagtgataatatttgttaatgatttgcattaaattgttagtagGTTTCTGGATCCATTTTCCAAAATGGAATGAGGTACTCGACTACTGTGCCCAATGATCCTGACACACATGATGATTTCAAATCCACTAATAAGCTTGAAA---
















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|298170152|gb|HO018776.1|HO018776
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|298174489|gb|HO014634.1|HO014634
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|207683666|gb|GD665529.1|GD665529
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|151403951|gb|EV273761.1|EV273761
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|298182900|gb|HO028113.1|HO028113
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|17153892|gb|BM143825.1|BM143825
EST:     TGTCCAGCATACTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|192323236|gb|FK017402.1|FK017402
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|192329314|gb|FK020233.1|FK020233
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTCCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|151397263|gb|EV267136.1|EV267136
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|13562443|gb|BG550663.1|BG550663
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTC-TTGTCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|31464055|gb|CD406083.1|CD406083
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|151410513|gb|EV280328.1|EV280328
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|9203815|gb|BE330039.1|BE330039
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|192306124|gb|FG996570.1|FG996570
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATAC--T--TACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|298190798|gb|HO032919.1|HO032919
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|208216921|gb|GE011215.1|GE011215
EST:     CTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: CTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|14012002|gb|BG726924.1|BG726924
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|10232984|gb|BE801872.1|BE801872
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|192306123|gb|FG996569.1|FG996569
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATAC--T--TACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|18039188|gb|BM307482.1|BM307482
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
EST: gi|17021277|gb|BM092311.1|BM092311
EST:     TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCT                         CTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT
genomic: TGTCCAGCATCCTTTTCAAGGGAATTGCAGCTCGTTCTTTCACCGCCCCTgtaacactga ... gtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggtcatgttttccttttgtaacagtatttgtcttcctttaatgtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAATGATCCTGACACACATGATGACTTCAAGCCAGCTAATAAACTTGAGAATT
                                            tgtcttc  CT-rich tract
                ttttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactgctataattgatagactagatgtttttgtttctcaagttgtaggtcatgttttccttttgtaacagtatttgtcttcctttaatgtcttcacagCTAACTAGGTCCTGTTATCATGGAATGAGATACTTTGCTACTGTATCAAATGATCCTGACACACATGATGACTTCAAGCCAGCTAATAAACTTGAGAATT

- tactgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctt