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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaaaccataatattgtatggttttttctctgcagcagtttacgtgagtaggtttctttctgtgtttgaatctaacaaaatttgattgtcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTCTGGCAGACACTCCTCTCATTCTTCTGGCCTGTGTTAA

Basic information

species Glycine max
transcript GLYMA18G07900.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G07900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G20920.1 (Arabidopsis thaliana), 3'ss of exon 2
gttaaaaccataatattgtatggttttttctctgcagcagtt-tacgtgagtaggtttctttctgtgtttgaatctaacaaaatttgattgtctt----cggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTCTGGCAGACACTCCTCTCATTCTTCTGGCCTGTGTTAA
  |          | |||| | ||||||  | ||    || | | | |   |  ||     | | |    |  | | |    ||||   | | ||    | | | || |||   || |||||||||||||| ||||||||||||||||| | |||||| ||||| || ||||| || ||  | || |||||||||||||| |   
--ttctctttggttcttgttttgtttttattttgagtaagatatgcattcatcagtgcaagtatatcagcgcttttgatttcatttttcttttttgatgcagGACGATCAATCTTTCTCTGAAAATGATGCCTTTTTTGCATGGACGTTCGAAAAACGGCATCCGCTATGGCAAACGCTTTTGTCCTTCTTCTGGCCTGTAT---

upper sequence: GLYMA18G07900.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 2
gttaaaaccataatattgtatgg---ttttttctctgcagcagtttacgtgagtaggtttctttctgtgtttgaatctaacaaaatttgattgtcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTCTGGCAGACACTCCTCTCATTCTTCTGGCCTGTGTTAA
 |  |      ||| |    |||   |  |   |||| | |  ||||     ||    || ||  |    |   |  |  |      ||| | | ||   ||||| ||  ||||||||||||||||||| ||||| |||||||| ||||| |||||    ||| | ||||||||||| |||||||| |||||||||||||| |
-tgcattgttcaatttctcttggaaatcatgcttctgtaaccatttatccaggtcaagttattgataccatattactttgcttg--ctgactctgttttacagGATCATTTATTTTCTGAAAATGATGCCTTTTTCGCATGGACATTTGTCAAACGGAGGCCATTGTGGCAGACACTTCTCTCATTTTTCTGGCCTGTGTTGA
















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|7042386|gb|AW472280.1|AW472280
EST:     CTGCGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTGTTTTCTGATAATGATGCTGTCTTTGCATGGACGTATGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298173185|gb|HO020169.1|HO020169
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|14259132|gb|BG882040.1|BG882040
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|208280739|gb|GE081021.1|GE081021
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCTTT
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTT
EST: gi|298170205|gb|HO018829.1|HO018829
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298174039|gb|HO017375.1|HO017375
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|151396851|gb|EV266724.1|EV266724
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298187066|gb|HO034215.1|HO034215
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|151409640|gb|EV279448.1|EV279448
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCACGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298169444|gb|HO020804.1|HO020804
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|298190464|gb|HO032585.1|HO032585
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA
EST: gi|19935346|gb|BQ080376.1|BQ080376
EST:     CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCT                         GAACAAGTATTTTCTGAAAATGATGCNNNNNNNGCATGGACGTTTGTAAAA
genomic: CTGGGAAGAAAAAGCTGTCTACCTGGCCTGCACATTTAGAAATTTTCCCTgtaagttttt ... tcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgagtaggtttctttctgtgtttgaatctaacaaaatttgattgtcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTCTGGCAGACACTCCTCTCATTCTTCTGGCCTGTGTTAA
                                          ttgtcttc  CT-rich tract
                         aatctaacaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaaccataatattgtatggttttttctctgcagcagtttacgtgagtaggtttctttctgtgtttgaatctaacaaaatttgattgtcttcggcagGAACAAGTATTTTCTGAAAATGATGCTTTTTTTGCATGGACGTTTGTAAAACGCCATCCACTCTGGCAGACACTCCTCTCATTCTTCTGGCCTGTGTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - tgtatgg
- - - - - - - - - - - - - - -ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa