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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaataattcttttagtgctcccttacaccacagtgcagagttgttttgaatgtcaaaagtacatgaaatctgaagttttgtccaaacaagttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA

Basic information

species Vitis vinifera
transcript Vv09s0002g02590.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G091494_T02 (Zea mays), 3'ss of exon 13
gtaaataattcttttagtg---ctcccttacaccacagtgcagagt-tgttttgaatgtcaaaagtacatgaaa-tctga-agttttgtc-caaacaagttg---tgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA
|||   |  ||| | | |    | |   | ||| |   ||   ||  | | |||  | |      |  ||| || ||||  | | ||||    ||| | |||   | ||||||||||| || |||||||||||||||||  | ||| |||| | ||||||||| || || |  || |||||||| || ||||||||||| ||| | ||||
gtatggatctctatcactaaatcactaatgcactatgttgtttagcctctcttgtgtttgttgctttgatgtaactctgttaatgttgttgtgaactacttggactacagAACAATGTTACTGAAATCAGAGCAGATGCATTAAAGTTGCTAGTCATGTTGAAAAGACCTGAGCCGCGTGCTGCAGCTACAATTGGAGCATGGTTGAACA

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G20980.1 (Glycine max), 3'ss of exon 14
---------------------------gtaaataattcttttagtgctcccttacaccacag-tgcagagttgttttga---atgtcaaaagtacatgaaatctgaagttttgtccaaacaagttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA
                            |    | ||  |||  ||||  | | ||| |  | |  | |     ||| |   || |      |  || |||| | |  |  |   |||   | |||  ||||||||  | |  || |||||  |||||||  |||||||||| |  || |||| | |||| ||||||||||| ||||||||| | ||||| ||||||||||
gtataaatgcttttatctacctcccttttttgcacttgcttt--tgcttgccttcactattgctataaatgctctttaattcattttgggcttttataaaatattacatcgttgacaacttacttggtcagAACAACCTTATGGAGATCAGGACAGATGCATTGAAGCTGCTAGTAATTTTGAGGCGGCCTGTTCCTCGTGCCGCTGCAACAGTAGGAGCCTGGCTTAACA

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G01550.1 (Glycine max), 3'ss of exon 13
---------------------------gtaaataattcttttagtgctcccttacaccacagtgcagagttgttt-tgaatgtcaaaagtacatgaaatctgaagttttgtccaaacaagt-------tgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA
                           ||    | ||  ||| ||||   | | ||   |  |  |   |  ||  |  || ||  |  |  || |||| | |  || |   |||   | |       ||  ||||||||  | |  || |||||  |||||||  |||||||||| |  || |||| | |||| ||||||||||| ||||||||| | ||||| ||||||||||
gtataaatgcttttatctacctcccttgttttcacttgcttttgtgccttcgt-cattgctataaatgctctttaattcatttcggacttttataaaatattacattgttgacaacttactccctccatggtcagAACAACCTTATGGAGATCAGGACAGATGCATTGAAGCTGCTAGTGATTTTGAGGCGGCCTGTTCCTCGTGCCGCTGCAACAGTAGGAGCCTGGCTTAACA

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G20980.2 (Glycine max), 3'ss of exon 13
gtaaataattcttttagtgctcccttacaccacag-tgcagagttgttttga---atgtcaaaagtacatgaaatctgaagttttgtccaaacaagttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA
      | ||  |||  ||||  | | ||| |  | |  | |     ||| |   || |      |  || |||| | |  |  |   |||   | |||  ||||||||  | |  || |||||  |||||||  |||||||||| |  || |||| | |||| ||||||||||| ||||||||| | ||||| ||||||||||
--ttgcacttgcttt--tgcttgccttcactattgctataaatgctctttaattcattttgggcttttataaaatattacatcgttgacaacttacttggtcagAACAACCTTATGGAGATCAGGACAGATGCATTGAAGCTGCTAGTAATTTTGAGGCGGCCTGTTCCTCGTGCCGCTGCAACAGTAGGAGCCTGGCTTAACA

upper sequence: Vv09s0002g02590.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G73020.2 (Arabidopsis thaliana), 3'ss of exon 14
gtaaataattcttttagtgctcccttacaccacagtgcagagttgttttgaatgtcaaaagtacatgaaatctgaagttttgtccaaacaagttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA
||||    | ||| |||| ||   ||           ||  ||  |  | |   |      | | ||||| |||||  | ||||        ||   |||| ||||||||  ||||| ||| || ||||  | |||||  | |  |   |    || ||  |||||||||||||||||||||||||||||||| | ||||
gtaa-cgttacttctagtactattttct---------caatgtcatccttagcttttggttttcttgaaaactgaatgtatgtc--------ttacacagAGCAATGTAATGGAAATAAGAACAAATGCTTTAAAGCTTTTGGTGACACTTCGAAGACCTCTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGTTAAACA

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|352782051|gb|FQ469349.1|FQ469349
EST:     TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTG                         AACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTG
genomic: TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTGgtaaataatt ... agttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTG
EST: gi|352777746|gb|FQ466799.1|FQ466799
EST:     TTATGATGTTGGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTG                         AACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTG
genomic: TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTGgtaaataatt ... agttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTG
EST: gi|110687623|gb|EE065247.1|EE065247
EST:     TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTG                         AACAATGTAACAGAAATCAGAGCAGATGCGCTAAAGCTGCTTGCCATGTTG
genomic: TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTGgtaaataatt ... agttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTG
EST: gi|110698301|gb|EE075671.1|EE075671
EST:     TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTG                         G
genomic: TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTGgtaaataatt ... agttgtgcag-
EST: gi|110698301|gb|EE075671.1|EE075671
EST:     TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTG                         G
genomic: TTATGATGTTTGCCTGTGCCTTCCCCCTTGCATTTGCCTTTGCGGCATTGgtaaataatt ... agttgtgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgaatgtcaaaagtacatgaaatctgaagttttgtccaaacaagttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA
           aaaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaataattcttttagtgctcccttacaccacagtgcagagttgttttgaatgtcaaaagtacatgaaatctgaagttttgtccaaacaagttgtgcagAACAATGTAACAGAAATCAGAGCAGATGCGCTGAAGCTGCTTGCCATGTTGAAGAGGCCAGTTCCTCGTGCTGCTGCAACAATTGGAGCTTGGCTTAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT