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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttaaaaccatcatattgtatggttttttctcctctgctgtttacccgattaggtttctttctgtgtttgaatctaacaatttgattgtctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTTTGGCAGACACTCCTCTCGTTTTTCTGGCCTGTGTTAA

Basic information

species Glycine max
transcript GLYMA08G45020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G20920.1 (Arabidopsis thaliana), 3'ss of exon 2
--atgttaaaaccatcatattgtatggttttttctcctctgc-tgtttacccgattaggtttctttctgtgtttgaatctaacaatttgattgtctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTTTGGCAGACACTCCTCTCGTTTTTCTGGCCTGTGTTAA
   | ||     | |  | |  | |  ||||   |    |     || | | |   | || | |    |  ||||| |  |    | |  ||   |   | | || |||   || |||||||||||||| ||||||||||||||||| | |||||| ||||| || ||||| || ||  | || || ||||||||||| |   
ttctctttggttcttgttttgtttttattttgagtaagatatgcattcatcagtgcaagtatatcagcgcttttgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT---

upper sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 2
atgttaaaaccatcatattgtatggttttttctcctctg-ctgtttacccgattaggtttctttctgtgtttgaatctaacaatttgattgtctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTTTGGCAGACACTCCTCTCGTTTTTCTGGCCTGTGTTAA
 ||       ||   | |  |     |  | || || |  |  |||| ||   |    || ||  |    |   |  |  |    ||| | | |||  ||||| ||  ||||||||||||||||||| ||||| |||||||| ||||| |||||    ||| | ||||||||||| ||||| ||||||||||||||||| |
-tgcattgttcaatttctcttggaaatcatgcttctgtaaccatttatccaggtcaagttattgataccatattactttgcttgctgactctgttttacagGATCATTTATTTTCTGAAAATGATGCCTTTTTCGCATGGACATTTGTCAAACGGAGGCCATTGTGGCAGACACTTCTCTCATTTTTCTGGCCTGTGTTGA
















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|6725798|gb|AW310197.1|AW310197
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298190292|gb|HO032413.1|HO032413
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCCTTTTTTGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|151394490|gb|EV264361.1|EV264361
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298182627|gb|HO031362.1|HO031362
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298191072|gb|HO038551.1|HO038551
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298167359|gb|HO012622.1|HO012622
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|213607340|gb|DB957148.1|DB957148
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298176469|gb|HO026704.1|HO026704
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|151405973|gb|EV275788.1|EV275788
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagtgttt ... tctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccgattaggtttctttctgtgtttgaatctaacaatttgattgtctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTTTGGCAGACACTCCTCTCGTTTTTCTGGCCTGTGTTAA
                                          ttgtcttt  CT-rich tract
                               taacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttaaaaccatcatattgtatggttttttctcctctgctgtttacccgattaggtttctttctgtgtttgaatctaacaatttgattgtctttggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTTTGGCAGACACTCCTCTCGTTTTTCTGGCCTGTGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - -ccatcat
- - - - - - - - - tgtatgg
- - - - - - - - - - - - - - - -ctcctct
- - - - - - - - - - - - - - - - - - - gctgttt