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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcatgcccttcacattagtgctaatttttcatattttttgtggcatattttacatgttcaactttctcatccattactgctgctaaaatttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA

Basic information

species Vitis vinifera
transcript Vv04s0023g00140.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G36200.1 (Glycine max), 3'ss of exon 7
----aaagcatgcccttcacattagtgctaatttttcatattttttgtggcatattttacatgttcaactttctcatccattactgctgctaaaatttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA
    ||  ||||  ||||   ||  || || | |     | |||| |      ||| |     | |||     | ||   |   |  |      | |  |||||  | ||  ||||||| || ||||||||| | |||||||||||||||||||||||||| |||||||||||||||  |
attaaatacatgttcttc---ttgttgatagtctagttaacttttggcatgtaattgtgtcattgcaatgaattgatttgtc-ttattatgtctaataaaacagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

upper sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
aaagcatgcccttcacattagtgctaatttttcatattttttgtggcatattttac---atgttcaactttctcatccattactgctgctaaaatttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA
          ||     | |   | ||   |  | |||   |     || || ||    || ||  | ||  |    | ||| |  ||   ||  |  || ||  | ||  ||||||| || ||||||||| | |||||||||||||||||||||||||| |||||||||||||||  |
tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtc-ttatttttgtctaa--taaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
















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|71861191|gb|DT010246.1|DT010246
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGAAAGAAGCTTCAATTCCTCGCAAAACATG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAA-CATG
EST: gi|110356881|gb|EC920025.1|EC920025
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|110724761|gb|EE100872.1|EE100872
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|110712695|gb|EE087976.1|EE087976
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|71865271|gb|DT014326.1|DT014326
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|161715809|gb|FC065164.1|FC065164
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|30135371|gb|CB920709.1|CB920709
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|30129653|gb|CB914992.1|CB914992
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
EST: gi|161719832|gb|FC065768.1|FC065768
EST:     GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCGTTGGTAGAAG                         CCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG
genomic: GTGGTTTTGATGCAAGAAGGATTAGCACATGTTATCCTCATTGGTAGAAGgtatgtgtag ... atttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatattttacatgttcaactttctcatccattactgctgctaaaatttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA
                                      tgctaaa  putative branch site (score: 2)
                                         taaaatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagcatgcccttcacattagtgctaatttttcatattttttgtggcatattttacatgttcaactttctcatccattactgctgctaaaatttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA

-aagcatg
- - - - cccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgctg