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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttatgaatatctatgccttgtccactttgttcaaacttttgattttaggatgtaaagtttttgtctatgtgctttctttaatatgttcataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA

Basic information

species Vitis vinifera
transcript Vv00s0313g00030.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 7
tatttatgaatatctatgccttgtccactttgttcaaacttttgattttaggatgtaaagtttttgtctatgtgctttctttaatatgttcataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA
  |  ||| | |  | | |  |      ||| |    |       | |  |    |     |    | ||     |||||        |  ||  | |||||||||||||| ||||| |||||||| || ||||| || | |||||||| | ||||||||||||||||  |||||   || ||||| || || ||  | |
-gtaaatggaaacttctccaatacattttttctgtggatccacagtgtatgtgcattgttgtgccctttaaaacatttctgcttctgatcaatttttcagGATATGGCTGCACATTCTGCTTGTGACTTCGGTGGTGGCAGAGCTGAGAGATTAGCTCTGGCTAAGTACAGACAAGTCATCTGGCAAGGGAGGGTATTAA

upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------tatttatgaatatctatgccttgtccactttgttcaaacttttgattttaggatgtaaagtttttgtctatgtgctt---tctttaatatgt------tcataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA
                                                          || |    || |  ||   |  |    |||||  ||  || |   | ||  |    | |  ||| ||| |  | |      |||  | | |      |  ||  |||||||||||| ||||||||||| || |||||||||||||| |||||||| ||||| || || || |||||| ||||    |||||||| || || || || |
gtattacactttctacacctaatttcttcaagaggtcatctatgtatacaaggttgtaatgttcacatcttcatttatccttttatttgtgaaacattgttgctctattaatacatgcatttatctgtcagttaataattttggtgtataaaacgttttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAACTGGCCCTTGCAAAGTATAGACAGGTGATTTGGCAAGGGAGGGTTCTTA

upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 7
----------------------------------tatttatgaatatctatgccttgtcca-ctttgttcaaacttttgattttaggatgtaaagtttttgtcta------tgtgctttctttaatatgttcataat-----------------------gcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA
                                  ||| | |  |  | | |    |   || |||||||  | | ||| ||||  | |   | | | ||  ||||      | ||| ||  |   || ||| |||||                       |||||||||||| ||||||||||| || |||||||||||||| |||||||| ||| | || || || |||||| ||||    |||||||| || || || || |
gtattactctttcttcatttgtttgataatcatctatgtgtacaagtttgtaatgttcgcatctttgttttatccttttatttgtgaaaaaacattgttgctctactaatatatgcatttatctgtaagttaataatttgggtgtataaattgttttatggcagGATATGGCAGCCCATTCGGCCTGCGATTTTGGTGGAGGAAAAGCTGAAAAATTGGCCCTTGCAAAGTATAGACAGGTTATTTGGCAAGGGAGGGTTCTTA

upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G65470.1 (Arabidopsis thaliana), 3'ss of exon 6
tatttatgaatatctatgccttgtccactttgttcaaa-cttttgattttaggatgtaaagtttttgtctatgtgctttctttaatatgttcataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA
  |  || |   | ||| ||     ||   | |||||| |||||| |  | |    ||    |||  || |  |  | |  ||  |||||| |||     ||| |||||||| ||||| || ||||||||||| ||||| ||||| ||||||||  |  |||| || ||  ||||||  |||||||| ||||||||  |||
-gtaaattatactttattcc--aatcatcctattcaaaacttttggtgattgttgttagttatttgatcaagattttcttcttgttatgtttata-----gGACATGGCTGCGCATTCAGCGTGTGATTTTGGCGGAGGCAAAGCCGAGAAACTCTCCTTGGCGAAATACAGACAAATGATTTGGCAAGGAAGAGTGTTGA

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|71857949|gb|DT007004.1|DT007004
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|161710023|gb|FC060239.1|FC060239
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|32267466|gb|CD716429.1|CD716429
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|30301036|gb|CB977830.1|CB977830
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|110703560|gb|EE080515.1|EE080515
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGA-GTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|46917634|gb|CN546963.1|CN546963
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|30326708|gb|CD009970.1|CD009970
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|32267671|gb|CD716634.1|CD716634
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|32247339|gb|CD713158.1|CD713158
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|30135746|gb|CB921084.1|CB921084
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|32268570|gb|CD717729.1|CD717729
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|29786039|gb|CB343476.2|CB343476
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|32270504|gb|CD719663.1|CD719663
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|71871778|gb|DT020833.1|DT020833
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|71876785|gb|DT025840.1|DT025840
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|161720195|gb|FC066766.1|FC066766
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|32267988|gb|CD717147.1|CD717147
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|30325113|gb|CD008375.1|CD008375
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
EST: gi|30324596|gb|CD007858.1|CD007858
EST:     GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAG                         GATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA
genomic: GCGAACAAGAGGCAGGAAAATTTGCTGTGCTACACCTTCGTTTTGATAAGgtatgactca ... cataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaggatgtaaagtttttgtctatgtgctttctttaatatgttcataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA
                                 ctttaat  putative branch site (score: 4)
                              tttctttaatatgttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttatgaatatctatgccttgtccactttgttcaaacttttgattttaggatgtaaagtttttgtctatgtgctttctttaatatgttcataatgcagGATATGGCTGCCCATTCGGCTTGTGATTTTGGTGGAGGTAAAGCTGAGAAACTAGCTCTGGCTAAGTATCGACAAACAATTTGGCAGGGAAGAGTCCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - -ctatgcc
- - - - - - - - - - - gtccact
- - - - - - - - - - - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - -gatgtaaa