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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT

Basic information

species Glycine max
transcript GLYMA15G06100.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 14
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT
                                                      |   ||| |    ||| | |   | | |||||||    |  ||   |    |||        || | | |||     |  | ||| | |       |||| ||| ||||| |  || ||||| ||||| ||  |||||||||| |||||   ||||||||||||||||||||||||||| |||||  |    | |||||  ||   |
------------------------------------------------------gtatattgaagaaattcactagctatcattttaaac-aacaaattccccactat------tcaacgaagtacaatgatcaaattactca-------aatcttttcagTGCCAAGATTTTCAACATATACCCTCGGAAAGGAGCAATTCTGGAAGGATCTGATGCAGATATTATCATCCTGAATCCCGAGAGGAGCTTTGTCATGGGT

upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaa--gctctttgtatagatgccaaaagtattactgatttttatttattt---atttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT
                                                        | ||  |   | |||      || | ||| |  ||||  |   ||| |||  |  ||      |  |   | | || | | |  ||||   ||  ||  ||   | | ||||||||||| ||||| ||||||||| ||||||||||||| ||| | || || |||||||||||||||||  | |||||||| |||| ||  ||||| |  
--------------------------------------------------------gtatatatgctctttcgaagcttctttttaatgttgaaaatttgctttttccaatgagcttttacttgaaagttatgtgtttgcatttgaaatgactttaagtttgtcagTGCTAGAATTTTCAACATATATCCACGGAAAGGAGCTATCCTTGCTGGCTCGGATGCAGATATTATCATATTGAATCCAAACTCAAGCTACGAGATTAGC

upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 11
gtatattttctgttaatcaaagtaaa-attagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT
||||  ||        ||||||| |  |||    |  || |    |   ||   | | |||     ||||   ||  | | | ||  ||||| ||     | |   |||  |  ||| | | |  | ||| ||| | || |  |||      ||  ||| ||||||||||||||||| || ||||||||||||||||| || ||| | |||||||||||||| || |||||  | || |||||||||| |||  | ||||||
gtatgctt--------tcaaagtgatcatttatgtagaggttccct---aaactgaaaaat-----gtataagatagtgtgttttacaatttaatctcagtttacctatcaa-accatatggaaaagtgagtttaacttttacatt------attttttcagTGCTAGAATCTTCAACATGTATCCAAGGAAAGGAGCAATACTTGCTGGATCTGATGCAGACATAATCATATTAAACCCAAATTCAAGCTTCCAAATAACT

upper sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S101_168V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttat---ttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT
                                                              |   | |  |   ||    ||| | | || |   |   ||| ||  |      ||  |   | || ||| |    | | | |   || | |||   | ||||||| | ||| |||||||| |||||  ||||||||||  | || ||||| ||||||||||| ||||||||  | || |||||| ||||   |   ||| | 
-------------------------------------------------------------tattttgtccaga-ataggcattgtgagtt-acacaatccttcgtgaattaaggaacggaggtccttattctgtgctttgtgtggattgtgcaact-tgttagTGCCAAAATATTCAATATTTATCCGCGGAAAGGAGCGGTGCTGCCAGGCTCTGATGCAGACATTATCATTTTGAACCCAAATGCAACTACTACTATATCC

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|58016987|gb|CX703729.1|CX703729
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATG                         TGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATGgtatattttc ... atcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
EST: gi|16349229|gb|BI974824.1|BI974824
EST:     AATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATG                         TGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
genomic: AATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATGgtatattttc ... atcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
EST: gi|37995958|gb|CF807547.1|CF807547
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATG                         TGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATGgtatattttc ... atcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
EST: gi|27445929|gb|CA953052.1|CA953052
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATG                         TGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATGgtatattttc ... atcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
EST: gi|298175277|gb|HO018158.1|HO018158
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATG                         TGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATGgtatattttc ... atcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
EST: gi|14991023|gb|BI316696.1|BI316696
EST:     TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATG                         TGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC
genomic: TCTGGCCAAATATCTGTCACTGACTATGTCCGGTTGACAAGCACTGAATGgtatattttc ... atcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT
                 tactgat  putative branch site (score: 2)
                                              tcatttt  putative PPT
              tattactgatttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttctgttaatcaaagtaaaattagcatccagttcttatagtaataaggagaattcagagtatttaattatttttattttaatttgatgaagctctttgtatagatgccaaaagtattactgatttttatttatttatttctacaatcattttagTGCTAGAATCTTCAATATATATCCAAGGAAAGGAGCTATTCTTCCAGGATCTGATGCAGATATTATCATCCTCAATCCAAATTCAACCTTTGAGATAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT