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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgaatgcaaacctcaatcaagttctacaagttctgttttggaattgttgtaatctcactggggttctctcctatcttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG

Basic information

species Vitis vinifera
transcript Vv02s0025g02140.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 6
--------------------gtatctgaatgca--aacctcaatcaagttctacaagttctgttttggaat-tgttgta-atctcactggggttctctcctatcttaacat-cagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG
                    | ||   | ||||  |  ||   |    ||||| |       ||   || | ||| ||  |  | | |    |  |    | ||| || |   |||||||||||||||| ||||||||||||||||| ||||| | ||| ||||||||||| ||   |||||| ||||||||||||||
gtatggctcattatctgactgcataaaagtgcacgatgcttgtttttcttctaaatccaaaattcatgactgtgtagtggactttaataatttgatgctttttctcaatacatagGTTTTTGAAGGTGAGAGGAGTCTCACAAAGGATTGCCGTCTGCTTGGGAAATTTGAACTGTCTGGAATTCCTCCAGCTCCAAG

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 6
--------------------gtatctgaatgca--aacctcaatcaagttctaca-----agttc-tgttttggaattgttgtaatctcactggggttctctcctatcttaacat-cagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG
                    | ||   |  |||  |  ||||||    ||||| |     | | | ||  |  | | ||| ||   ||        |  |  | | ||| || |   ||||||||||||| || ||||||||||||||||| ||||| | ||| ||||||||||| ||   |||||| ||||||||||||||
gtatggctcattattcaactgcattaaagggcacgatgctcaattgtcttctaaattcaaaatgcatgactgtgtagtgtagtggactttaataattgatgccttttctcaatacatagGTTTTTGAAGGGGAGAGGAGTCTCACAAAGGATTGCCGTCTGCTTGGGAAATTTGAACTGTCTGGAATTCCTCCAGCTCCAAG

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 6
----------------------------------gtatctgaatgcaaacctcaatcaagttctacaagttctgttttggaattgttgtaatctcactggggttctctcctatcttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG
                                     ||| ||| ||||   ||      |      |  | || |  || ||||   | |    | |        ||  | |||||| | |||||||| |||||||| ||||||||||||||||| || || |  || ||||||||||||||   |||||| || |||||||||||
gtacggtgccattaaagggcatgatgcgtgtttttcttctaaatccaaaatgcaccactatctggtgaactatgat--gggattgacttgaaacgattca---ctgcttttttcttaata-cagGTTTTCGAAGGTGAGAGGAGTCTCACAAAGGATTGTCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCACCAGCTCCAAG

upper sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 6
------------------------------gtatctga-atgcaaacctcaatcaagttctacaagttctgttttg--gaattgttgtaatctc-actggggttctctcctat--cttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG
                              |    |||   |      ||    || |   | | |      | |   ||| | |       |  ||| |  ||| || || |  ||||| | |||||||| ||||| || ||||||||||||||||| ||||| |  || ||||||||||||||   |||||| |||||||| |||||
gtatggtgccattattcaatttgcattaaagggcatgatgcgtgtttttcttctaaatctaaaatgcatgactgtagtgaactatgacggggttgactcgaattcactgctttttcttaata-cagGTTTTCGAAGGCGAGAGGAGTCTCACAAAGGATTGCCGCCTTCTTGGGAAATTTGATCTGTCTGGAATTCCTCCAGCCCCAAG

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|110708297|gb|EE085674.1|EE085674
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|351048169|gb|FQ442139.1|FQ442139
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|110379529|gb|EC944729.1|EC944729
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|352799018|gb|FQ480867.1|FQ480867
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|33404779|gb|CF210406.1|CF210406
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|351026509|gb|FQ428521.1|FQ428521
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|352794236|gb|FQ479478.1|FQ479478
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAGGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|110700835|gb|EE077835.1|EE077835
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAT                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|351033837|gb|FQ447875.1|FQ447875
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|110378299|gb|EC943423.1|EC943423
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|351044960|gb|FQ449214.1|FQ449214
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|110719342|gb|EE097207.1|EE097207
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|110702839|gb|EE079171.1|EE079171
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|28968374|gb|CB347407.1|CB347407
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|349825531|gb|FQ419448.1|FQ419448
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|352790752|gb|FQ478300.1|FQ478300
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|351055860|gb|FQ452325.1|FQ452325
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|30296579|gb|CB973373.1|CB973373
EST:     TTCAAGTTTTCACTACTTACCAGGATCAGCAGACCCCCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|30298100|gb|CB974894.1|CB974894
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCCCCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
EST: gi|110384327|gb|EC948755.1|EC948755
EST:     CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAG                         GTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA
genomic: CTCAAGTTTTCACTACTTACCAGGATCAGCAGACCACCGTCTCCATTCAGgtatctgaat ... ttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttttggaattgttgtaatctcactggggttctctcctatcttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG
                                           tcttaac  putative branch site (score: 2)
                                 ttctctcctatctt  CT-rich tract
                                         tatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgaatgcaaacctcaatcaagttctacaagttctgttttggaattgttgtaatctcactggggttctctcctatcttaacatcagGTTTTTGAAGGTGAAAGGAGTCTCACAAAGGACTGCCGACAGCTCGGGAAATTTGATCTTAATGGAATCCCTCCAGCTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC