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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttggtgttcaggtatcttggtttggcattaatttaaatttatcatctgatttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG

Basic information

species Vitis vinifera
transcript Vv01s0026g01640.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G02540.1 (Glycine max), 3'ss of exon 4
gtatcttggtgttcaggt-atcttggtttggcattaatttaaatttatcatctgatttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG
        || | |  || || ||   ||   | |    |||       |  || || | |  | |  |  |  |   ||||| |||||||||||||| |  ||||||||||| || |||||||||||||| || ||||||||||||||||| ||||| ||||||||||| ||||| |
--------gtatccctgtcattttaaattcagagtggagtaag------acatgcttaatctgtttgcttttactttctagGCTATGTCAGCTTATGGGTATGAGATAGTTCAGACGCTTATTGTGGATATTGAGCCAGATGAGCATGTGAAGAGAGCCATGAATGAGATTAATGCTG

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G02500.1 (Glycine max), 3'ss of exon 4
--gtatcttggtgttcaggtatcttggtttggcattaatttaaatttatcatctgatttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG
   || | |  || |    | | ||   ||   | |  | ||     |    || | |     |||||||  |      ||||| |||||||||||||| | |||||||||||| || |||||||||||||| || |||||||||| |||||| ||||| ||||||||||| || || |
gtatacccttttgcttta-tgttttaaattaagaatggtgtagg---acatccttaatctgttttcttttactttc---tagGCCATGTCAGCTTATGGGTACGAGATAGTTCAGACTCTTATTGTGGATATTGAGCCAGATGAGCGTGTGAAGAGAGCCATGAATGAGATCAACGCTG

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G16270.1 (Glycine max), 3'ss of exon 4
--gtatcttggtgttcaggtatcttggtttggcattaatttaaatttatcatctgat--ttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG-
   |   ||    ||   |||| |  |||  | | ||       ||    | || ||  ||   |   |  ||   |||   |||||||||| |||||||| |  |||||||| || || |||||||||||||| ||||| ||||||| |||||| ||||| ||||| ||||||||||| | 
tgattgattcccttttgtgtatgtgtgttgaggactaga--gggttagcaaccttatggtttttaacttgctgtgcatgtgaaggCAATGTCTGCTTATGGGTATGAGATAGTCCAGACTCTTATTGTGGATATTGAACCGGATGAGCGTGTGAAGAGAGCCATGAACGAGATAAATGCTGG

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G02550.1 (Glycine max), 3'ss of exon 4
gtatcttggtgttcaggtatcttggtttggcattaatttaaatttatcatctgatttaacattcttt-tggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG
        || ||      | |   |||    |||| ||||   |        || |||  |  ||  |  |  |   ||||| |||||||| ||||| | |||||||||||| || |||||||||||||| |  || |||||||||||||| | ||| ||||||||||| ||||| |
--------gtattt---cctttcattttatttttaaattaagaatggagaactatgtaatctgtttggttttactttctagGCTATGTCAGCATATGGGTACGAGATAGTTCAGACTCTTATTGTGGATATTGTGCCGGATGAGCATGTGAAGAAAGCCATGAATGAGATTAATGCTG

upper sequence: Vv01s0026g01640.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G04950.1 (Glycine max), 3'ss of exon 3
gtatcttggtgttcaggtatcttggtttggcattaatttaaatttatcatctgatttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG
         |   |   ||  || ||||   |||||        ||  |  |  || | |  | || | || ||   ||||| |||||||| ||||| |  ||||||||||| || |||||||||||||| || |||||||||| |||||| || || |||||||| || ||||| |
------gtatacccttttacttttgttttaaattaaaaatggagtaggacatctttaatctgttttcttgtcatttctagGCTATGTCAGCATATGGGTATGAGATAGTTCAGACTCTTATTGTGGATATTGAGCCAGATGAGCGTGTGAAGAGGGCCATGAATGAAATTAATGCTG

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|161721397|gb|FC070773.1|FC070773
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|26262182|gb|CA813245.1|CA813245
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110400525|gb|EC967091.1|EC967091
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110724693|gb|EE100742.1|EE100742
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110423580|gb|EC989927.1|EC989927
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110425409|gb|EC991794.1|EC991794
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110697820|gb|EE075232.1|EE075232
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110382334|gb|EC939189.1|EC939189
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110687599|gb|EE065191.1|EE065191
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110389091|gb|EC953904.1|EC953904
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|161715489|gb|FC069052.1|FC069052
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
EST: gi|110375966|gb|EC940998.1|EC940998
EST:     TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAG                         GCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC
genomic: TTGAACAGAAGAATGAAATAGCGAAAGCTGTGGAAGAGGAACTTGAAAAGgtatcttggt ... tgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggcattaatttaaatttatcatctgatttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG
                            atttaac  putative branch site (score: 3)
      attaatttaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttggtgttcaggtatcttggtttggcattaatttaaatttatcatctgatttaacattcttttggtgatgcatagGCAATGTCAGCTTATGGATTCGAGATAGTTCAAACACTTATTGTGGATATCGAACCAGATGAGCATGTGAAAAGAGCAATGAATGAGATAAATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA