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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA

Basic information

species Vitis vinifera
transcript Vv09s0002g00170.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 9
---------------gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttg---gctgttattttgggttcttggtttttctcatattctttttccacatt-cagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
                | |||      ||||   ||    || |   | | |    |  | |       |     || | || |        |||  || || || | || | ||     || ||||||| || ||||| ||||| ||||| |||||||| |||||||| ||||| || ||| |||| |||||||| |||||||||||||||||| | || |||||
gtaactggaagaactttgaaacttcgttctgggtggtttcttctagatttgtttgttatagtctccacctcaaaagcggataatgctaagctttg--ttctcacaaactcctgtttgctgttacagGAGCTGATATAAGGAGTGTCTGCACAGAAGCTGGCATGTATGCGATTCGCGCCCGACGGAAAACAGTGACTGAGAAGGACTTCCTTGATGCTGTAAACAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g09290.1 (Oryza sativa), 3'ss of exon 6
--------gtaaaatacttatctgaagggcacgttgtctttgtatactctccattg-atggttttggctgttattttgggttcttggtttttctcatattc-----tttttccacatt----cagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
            ||| |||   |||  |  |    |||| ||  || | ||  ||  |||   ||     |||   |   || ||   ||||||||  ||      ||| |     ||    |||| ||||||||| | ||||||||||| || ||||| ||||| || || || || || |||||||| ||||| |||||||| ||| | ||  | ||||| ||
gtaagtgccgggaattcttgcatgacaga-atccagtctctggctagtttctgttccatgtcatttatctttaacctcctttttt---ttttctcacgtttggctatttgtgtttgttggaacagGGGCCGACATACGGAGTGTGTGCACGGAGGCTGGCATGTACGCCATCCGCGCTCGCAGGAAGACGGTGACAGAGAAGGATTTCTTGGACGCGGTGAATAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 9
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattcttttt--ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
        | | |||                ||| | |   | | || | | ||| ||  |||  |   | ||  |  |||  |    || ||||||       | |||||||||| ||||| || || |||||||||||||| |||||||||||||||||  |||||||||| ||||| ||||| |||||||||||  |||| || ||
--------cctttcttccctatgacccacgattgaacatcgtgc-ttcaggctttgggtagtttatagagattggttttttgaccaggatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 9
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattcttttt--ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
          | ||||     | | || |        || | | |||||   ||  |    ||||   |  |  ||  |||  || | || ||||||       | |||||||||| ||||| || || |||||||||||||| |||||||||||||||||  |||||||||| ||||| ||||| |||||||||||  |||| || ||
---------atttctgccactccctttcttccctatgacccacgattgaacattgggtagtttatagagattggtttttttgacttagatactttttggttctctccagGAGCCGATATAAGGAGCGTTTGCACTGAAGCTGGTATGTATGCTATTCGAGCCAGAAGGAAGACCGTGACAGAGAAAGACTTCCTTGACGCAGTTAATAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattcttttt-ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
      | || || |        | |||   |   | | | |   || ||| ||| || |    || | |    | | ||| |   | || ||||||      | ||||||| || ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||| || || ||||| |||||||||||| |||| || ||
---tttttctcatttcctaaa-gctttgctatccaacattgttgcttcatgctttaggat----ttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatat-tctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
      | |||   ||   | ||  | || ||   ||||    |  |||   | |  ||| | ||  | |    | | ||| |   | ||  |||||      | ||||||| || ||||| ||||| ||||| ||||| || ||||||||||| || || || |||||||| || || ||||| |||||||||||| |||| || ||
---gtgtgctt-catgctagacat-tggttttctgatacatatc--tgacattgtgtgct-tcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
--gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
   | |   |     ||| ||       |    | ||    |   ||    | || |    | | |      ||   ||        ||  | |||  ||    | ||||||| || ||  | |||||||| || || || || |||||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||  | || |||||
gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactga-----agcaagtgcttgatc----tgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgt--tattttgggttcttggtttttctcat----attctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA------
                    ||| |      | | ||  | || | |  ||  ||   | |   || | ||   |||       | |||          |  |  |  | ||||||| || ||  | |||||||| || || || || |||||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||  | || |||||      
-------------------tgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT

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|352781883|gb|FQ469180.1|FQ469180
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|22014898|gb|BQ799932.1|BQ799932
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|32247817|gb|CD713636.1|CD713636
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|110722901|gb|EE099603.1|EE099603
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|71877945|gb|DT027000.1|DT027000
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|33404512|gb|CF210139.1|CF210139
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|110391747|gb|EC956746.1|EC956746
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|32247872|gb|CD713691.1|CD713691
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|32246398|gb|CD712217.1|CD712217
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|32246414|gb|CD712233.1|CD712233
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|71878819|gb|DT027874.1|DT027874
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTG
EST: gi|46917703|gb|CN547032.1|CN547032
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|22013526|gb|BQ798560.1|BQ798560
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|110382613|gb|EC946924.1|EC946924
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|32272322|gb|CD721481.1|CD721481
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|110381975|gb|EC938156.1|EC938156
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
EST: gi|27586753|gb|CB009448.1|CB009448
EST:     GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTG                         GAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG
genomic: GAGGGATATCCGTTTTGAACTTTTGGCTCGTCTTTGCCCAAACTCAACTGgtaaaatact ... ccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggctgttattttgggttcttggtttttctcatattctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA
                   ttcttggtttttctca  CT-rich tract
                                  atattcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA