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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtaaaattgtaccccaataagctctactatgccgttttaatattcatttctgttttcaagtgcttactatgataggacctgttttctctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGAACTACAGTAGAGTTGCCAATTATGCACCAGCATATGCAATGAATGATGA

Basic information

species Glycine max
transcript GLYMA11G18760.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G18760.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g00800.t01 (Vitis vinifera), 3'ss of exon 1
------ttagtaaaattgtaccccaataagctctactatgccgttttaatattcatttctgttttcaagtgcttactatgataggacctgttttctctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGAACTACAGTAGAGTTGCCAATTATGCACCAGCATATGCAATGAATGATGA
      ||  |    ||  |  |   ||     |  | |  |  |||  ||  | ||    |||| |  ||| |       ||   | ||   | |  | |||||||| | ||||| || || ||| | |||||||| || |||||||| |||||||||||  | | ||| ||| | ||||| || ||||||||||||||||||||
atattttttattgctttccatactcgtacatgtttttctctctgttttttaccctttctgattttaagatgcatgtc----taatgcttggcattt--taatccagGGCGGATCCCATTTTCATACCTTGAAGATATTCAGATGAGGTTCATGAAGAACTATGGGAAAGTGGCCCACTATGCTCCTGCATATGCAATGAATGATGA
















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|298197870|gb|HO039409.1|HO039409
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|19270491|gb|BM886747.1|BM886747
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|213596206|gb|DB960166.1|DB960166
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|27808898|gb|CB063320.1|CB063320
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|209707880|gb|BW662086.1|BW662086
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|254321070|gb|GR827519.1|GR827519
EST:     CGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|5057629|gb|AI736105.1|AI736105
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|16348943|gb|BI974538.1|BI974538
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|24136750|gb|BU927260.1|BU927260
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|7286109|gb|AW598596.1|AW598596
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|192321054|gb|FK013528.1|FK013528
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|11413060|gb|BF425080.1|BF425080
EST:     CGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|151394906|gb|EV264777.1|EV264777
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCCAATGAGGTTTACGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|57575163|gb|CX548138.1|CX548138
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
EST: gi|15662923|gb|BI700286.1|BI700286
EST:     CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAA                         GGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA
genomic: CCGATCCGATGGCATCACCTACGTCTGTATGGCCAACGACACCTTCGGAAgtgagttctt ... ctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttctgttttcaagtgcttactatgataggacctgttttctctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGAACTACAGTAGAGTTGCCAATTATGCACCAGCATATGCAATGAATGATGA
                  tgcttac  putative branch site (score: 2)
                                   cctgttttctctttat  putative PPT
          ttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtaaaattgtaccccaataagctctactatgccgttttaatattcatttctgttttcaagtgcttactatgataggacctgttttctctttatccagGGAGAATCCCTTTCTCGTACTTGGAAGATATCCAAATGAGGTTTATGAAGAACTACAGTAGAGTTGCCAATTATGCACCAGCATATGCAATGAATGATGA

- - - - - - tacccca
- - - - - - - - - - - - - - -ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttt