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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaatgggtgtaagtttgagaaaaataaaggaagaaaaaggtgacctaactggtatgttgtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGATGTGCAATGGTGGAATCCAGAGGAACTCAAGTTCTACTACGACGGGCAA

Basic information

species Vitis vinifera
transcript Vv01s0011g06290.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G09880.2 (Glycine max), 3'ss of exon 6
-----------gtataaaatgggtgtaagtttgagaa-aaataaaggaagaaaaaggtg-------acctaactggtatgttgtttgtgc---------agTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGATGTGCAATGGTGGAATCCAGAGGAACTCAAGTTCTACTACGACGGGCAA
            |  | | |  || || | ||    | | ||| | | ||  |||  |        | |||||   ||  || | ||| |         ||| ||||||||||| ||||| | || || ||||||||||| |||||||| | |||| | |||||||| ||||| ||  | |||||||||||||| || |||
gtttgtttattttcaagagtatgtatatgcttagttacatatatatgtagtgaaaattagagtaatatctaaccattaaattatatgtacttgaatttcagTGCAATTCAATTTTTGACTTGCGGGGGAGGGTCAAAGGCGTGGAGGGGTGTTGTGAACTGGTGGAAGCCAGAAGAGATGAAGTTCTACTACGATGGCCAA

upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G26920.1 (Glycine max), 3'ss of exon 8
-----------------------gtataaaatgggtgtaagtttgagaaaaataaaggaagaaaaaggtgacctaactggtatgt-tgtttgtg-----cagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGATGTGCAATGGTGGAATCCAGAGGAACTCAAGTTCTACTACGACGGGCAA
                        || |  |||  ||||   || ||  | |||   | ||  |||  | |  ||||   ||  | ||    ||     |||| ||||||||||| || |||| || || ||||||||||| |||||||| | |||| | |||||||| ||||| ||  | |||||||||||||| || |||
gttttcctttagatcgatcttgcatacatgatgcatgtatagtttagttacatat--gtagtgaaaattaatttaaccattaaatatgcacatgaatttcagTGCAATTCAATTTTTGGCTAGCGGGGGAGGGTCAAAGGCTTGGAGGGGTGTTGTGAACTGGTGGAAGCCAGAAGAGATGAAGTTCTACTACGATGGCCAA

upper sequence: Vv01s0011g06290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G25230.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------gtataaaatgggtgtaagtttgagaaaaataaaggaagaaaaaggt---------gacctaac-tggtatgttgtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGATGTGCAATGGTGGAAT-CCAGAGGAACTCAAGTTCTACTACGACGGGCAA
                          |||||||       |  |||||    ||    |  |  ||| || |         ||  |||| |  |||  |  || ||||| |||||||| ||||| || |||||||| ||||||||||||||||| ||| || | |||| |   ||  ||||||||  | || || | |||||| || |||
gtaacaacgattaatagttatatggagtataaaccaaacctgtgtttggatgaagcggataacaaaagagataaagttgtggatttaacattttattataattttgcagCCCAATTCAGTTTCTAACGAGTGGTGGTGGGTCAAAGGCATGGAGAGGCTAT-TACAATTGGACAACACCAGAGGATATGAAATTTTTCTACGATGGACAA

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|56688100|gb|CX126003.1|CX126003
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688146|gb|CX126049.1|CX126049
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688532|gb|CX126435.1|CX126435
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|30324780|gb|CD008042.1|CD008042
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110361763|gb|EC925259.1|EC925259
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110382161|gb|EC938649.1|EC938649
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688821|gb|CX126724.1|CX126724
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688240|gb|CX126143.1|CX126143
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110405384|gb|EC970925.1|EC970925
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|30330531|gb|CD013793.1|CD013793
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110378747|gb|EC943895.1|EC943895
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|30128027|gb|CB913366.1|CB913366
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|30127523|gb|CB912862.1|CB912862
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|34542274|gb|CF510506.1|CF510506
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAATGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110427573|gb|EC994020.1|EC994020
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688741|gb|CX126644.1|CX126644
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|30125391|gb|CB910730.1|CB910730
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688020|gb|CX125923.1|CX125923
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|349811174|gb|FQ406162.1|FQ406162
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTG
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTG
EST: gi|71867743|gb|DT016798.1|DT016798
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110701614|gb|EE079386.1|EE079386
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|30126050|gb|CB911389.1|CB911389
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688831|gb|CX126734.1|CX126734
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688837|gb|CX126740.1|CX126740
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688383|gb|CX126286.1|CX126286
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688239|gb|CX126142.1|CX126142
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|110385343|gb|EC949857.1|EC949857
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|27586836|gb|CB009531.1|CB009531
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
EST: gi|56688885|gb|CX126788.1|CX126788
EST:     TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAG                         TCCAATTCAATTTCTGACGAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA
genomic: TACATAAACGGACATGACCATTGCTTGGAACACATCAGTTCCCCCGACAGgtataaaatg ... gtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgagaaaaataaaggaagaaaaaggtgacctaactggtatgttgtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGATGTGCAATGGTGGAATCCAGAGGAACTCAAGTTCTACTACGACGGGCAA
                             acctaac  putative branch site (score: 2)
      aaaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaatgggtgtaagtttgagaaaaataaaggaagaaaaaggtgacctaactggtatgttgtttgtgcagTCCAATTCAATTTCTGACTAGTGGTGGCGGGTCAAAGGCATGGAGGGGCGATGTGCAATGGTGGAATCCAGAGGAACTCAAGTTCTACTACGACGGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA