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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccattctccctcttcttggtttactgatgtactttttttttattacaataaaatttcaagtggagcaagagatgctgaataataaccttgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07960.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 1
ccattctccctcttcttggtttactgatgtact-ttttttttattaca--ataaaatttcaagtggagcaagagatgctgaataataacc---------ttgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG
            |  ||   | |  | ||| || || ||  |  ||||  | |   |      || |  | ||  || |||  | | |||         || |  ||   |||||||||||||||| || || |||||||| |||||||| ||||| || ||||| |||||||||||| |||| ||||||||||| || ||||||||||||
------------tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgttattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G12350.2 (Glycine max), 3'ss of exon 1
ccattctccctcttcttggtttactgatgtact-ttttttttattaca--ataaaatttcaagtggagcaagagatgctgaataataacc---------ttgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG-
            |  ||   | |  | ||| || || ||  |  ||||  | |   |      || |  | ||  || |||  | | |||         || |  ||   |||||||||||||||| || || |||||||| |||||||| ||||| || ||||| |||||||||||| |||| ||||||||||| || |||||||||||| 
------------tgtttatctaatcggtgttctattcttggtgctacatgacatggtgatgtatgaacaaggatgtgttgaccagtgacccattgcttgttattgctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCTGGTGATGAGG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 1
ccattctccctcttcttggtttactgatgtactttttttttattacaataaaatttcaagtggagcaag--agatgctgaataataacct--tgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG
    | | | |||  ||||| | ||  | |   |  |   |   |   | |  ||| ||   |     |    ||  |||    |  | |  | | |||   |||||||||||||||| || || |||||||| |||||||| ||||| || ||||| |||||||||||| |||| ||||||||||| || || || ||||||
----tgttcatctgattggtgttctattcttggtgctacatggcatggtgatgtttgaacaaggatgtgttgaatagtgacccgttgcttgttatttctcttagGTTCTTGGTGTGGAGAAAACAGCATCTCAACAGGAAATAAAGAAGGCATACTACAAGTTGGCATTGAGGCTGCATCCTGATAAGAACCCCGGCGATGAG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 1
------------------ccattctccctcttcttggtttactgatgtactttttttttattacaataaaatttcaagtggagcaagagatgctgaataataaccttgtgtc---------------ttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG-
                   | || ||  ||   ||  |||  | ||| | | |||   ||||  |||  |||| |  |||  |  |  | || |  || || || |||| |                ||  |||||||||| ||||| |  ||||| |||||||||||||| ||||| || ||||| |||||||| |||||||| || || ||||| || |||||||||||  
gtaccctaaaaaattcatgctttttctttcgctttcctttgataatggattatttcactattcaaattcaatt-cgcgtgttgttactg-tgatatattatgactttgtttgacggtggttgagtggttgtagGTTCTTGGCGTGGAGAGAACGGCGTCTCAGCAGGAAATAAAGAAGGCGTACTACAAGTTGGCGTTGCGGCTTCACCCCGATAAGAACCCTGGTGATGATG

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|351015510|gb|FQ447339.1|FQ447339
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAAGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|349825564|gb|FQ419481.1|FQ419481
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAAGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|352794289|gb|FQ479531.1|FQ479531
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|351028672|gb|FQ446345.1|FQ446345
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|351054628|gb|FQ456825.1|FQ456825
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAACAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|110686833|gb|EE063714.1|EE063714
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAAGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|349827514|gb|FQ422382.1|FQ422382
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|351048863|gb|FQ431528.1|FQ431528
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|351023284|gb|FQ432667.1|FQ432667
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
EST: gi|351040488|gb|FQ434621.1|FQ434621
EST:     AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAG                         GTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC
genomic: AAGAAGAGTATGTTAGTCAGTCTTCCACAAACGAGAGGAGCCTGTACGAGgtatgtgaaa ... tgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataaaatttcaagtggagcaagagatgctgaataataaccttgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG
                                  taataac  putative branch site (score: 1)
                              tgaataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccattctccctcttcttggtttactgatgtactttttttttattacaataaaatttcaagtggagcaagagatgctgaataataaccttgtgtcttacagGTTCTTGGTGTGGAAAAGACGGCATCTCAGCAGGAAATTAAGAAAGCTTACTATAAGTTGGCATTGCGGCTCCATCCTGATAAAAATCCTGGTGATGAG

ccattct
- - - -ccctctt
- - - - - - - - - - - -ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataacc