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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccagtatcttttgatgaaacgtctgtcatcagttcatatattttttatgagaagccaacttcattgttttaaatagtcttccgatctactttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAACAGTAACTTGGCTGTCAATCCTTCTTATGTTCGATCATGGTTAGATGTTT

Basic information

species Glycine max
transcript GLYMA11G18710.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0080g00880.t01 (Vitis vinifera), 3'ss of exon 10
tcccagtatcttttgatgaaacgtctgtcatcagttcatatattttttatgagaa-gccaacttcattgttttaaatagtcttccgatctactttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAACAGTAACTTGGCTGTCAATCCTTCTTATGTTCGATCATGGTTAGATGTTT
| |   |||   | |||  |         ||     || || ||  ||||||    |   |  |  || | ||         |    ||| | ||  ||||||||| |||||||| ||| | |||||||||||||| || ||||||||  |||||| ||||||||| || ||||||||  ||| ||| |||||  || | |
tgctgatatgcat-gatagagtcaaaaaaattttaacaaattttagttatgactttgttcatctggttttatttctctaatgtaatctctcccttacacagAGGCACATCTATGGCCATGAGGGAAAGAACATTCAAATTTTTGCAGATGACAGTAGCTTGGCTGTTAACCCTTCTTACATTCAATCGTGGTTGCATCTGT
















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|18733631|gb|BM527732.1|BM527732
EST:     GTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: GTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|17400577|gb|BM177359.1|BM177359
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|58023069|gb|CX709810.1|CX709810
EST:     TGAAGCGGCTA-TGTTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: TGAAGCGGCTATTG-TCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|21993710|gb|BQ785238.1|BQ785238
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|10848066|gb|BF070623.1|BF070623
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|33388989|gb|CA852196.1|CA852196
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|254343175|gb|GR859337.1|GR859337
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|57574504|gb|CX547479.1|CX547479
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC
EST: gi|151406228|gb|EV276043.1|EV276043
EST:     ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCG                         AGGCATATCTATGGACATCAAGGAA-GAACATTCAGATCTTTGCAGACA-C
genomic: ATGAAGCGGCTATTGTCAGAAGTGTGAAATTAATTGCTGAGAGTCTTGCGgtaagattaa ... ctttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgagaagccaacttcattgttttaaatagtcttccgatctactttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAACAGTAACTTGGCTGTCAATCCTTCTTATGTTCGATCATGGTTAGATGTTT
                                         tctactttct  CT-rich tract
                ttcattgttttaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccagtatcttttgatgaaacgtctgtcatcagttcatatattttttatgagaagccaacttcattgttttaaatagtcttccgatctactttctacagAGGCATATCTATGGACATCAAGGAAAGAACATTCAGATCTTTGCAGACAACAGTAACTTGGCTGTCAATCCTTCTTATGTTCGATCATGGTTAGATGTTT

tcccagt
- - - - - - - - - - - -tctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacttc