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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag

Basic information

species Vitis vinifera
transcript Vv05s0049g01230.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 3
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgg--gcag
|| || || ||||| || || || || || ||||||||||| ||||| |||||||| || || || ||||||||||||||| |||||||||||   | || ||  | | |        ||  | || ||   |   | |  |  |||||  |||| | ||| | |    ||||
GCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATTgtaagta-tatctttttccaaaataaacaaaaat-gtgttgttgggaa--tgtagtaacttagtattgaggatttcttttattgcag

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G121942_T03 (Zea mays), 5'ss of exon 3
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag
|| || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||||||||| ||| || |||| |        |     | |  ||| ||| |   |   | ||||  |||| |   || | |   |||
GCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaagatgctactaaatt-ataagacatcaatgcttaattttgtttccttattta--cag

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G121942_T01 (Zea mays), 5'ss of exon 3
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag
      |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||||||||| ||| || |||| |        |     | |  ||| ||| |   |   | ||||  |||| |   || | |   |||
-----CGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtatcctgttctttttgtaacaaaagatgctactaaatt-ataagacatcaatgcttaattttgtttccttattta--cag

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G106574_T01 (Zea mays), 5'ss of exon 3
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag
|| || ||||| || || || ||||| |||||||||||||| ||||| ||||||||||| || || |||||||| |||  ||||||||||||| |||||| |||| |       |    | | |  ||| ||| |   ||    ||||   ||    || | |   |    
GCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATTgtaagtaccctattctttttgtaacaaatcatgttactgaatt-atatgacattaccgcttaatgttttccttatttacag----

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 2
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttg-tcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag------------
||||||||||||||||| || || ||||||||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||||| |||  |    | | |    |||      |  |   ||||||| ||   || | | |      |||| | || | |||| ||              
GCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATTgtgagtttctctctctctcccttttccccaattttttgtttatttttaaaattatttgttaaccgtttgtttttctttgtgtgcgtgtgtgtgtgcag

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 2
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattatttt-----agatttggttgtcatcattttatttataggtttttctttcttagatttgatgt---tttgtgtgggcag
|| |||||||||||||| || || || ||||| |||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||||| |||   || |   | |     |  |||  |||| |   ||  |  |||   ||  ||||| ||   |||   ||   | |||||  ||||
GCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATTgtgagttttctctctctcttccccaattttttttgttaattttaaaactatttattaatcttttttttcttttgcgtgggtgtgtgtctgcag

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 2
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagattt--ggttgtcat---cattttatttataggtttttctttcttagatttgatgttttgtgtgggcag
|| |||||||||||||| || || || |||||||||||||| ||||| |||||||||||||| ||||||||||| |||| |||||||| |||  | | | |||||||  ||    || | ||   |||| | ||||| || |  |  ||  | || |||  ||||     |  |||
GCAAGTGATAGGTTTAACATCAATTCTCAGCTTGAGCATCTTCAAGCTAAATATGTTGGAACCGGTCATGCTGATTTGAGTAGATTgtgagtttcttttgattttagtgttcaaatttttatatgcattgtttttattggctactaatttgtggaattg--gtttaaatggtacag

upper sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G23325.1 (Arabidopsis thaliana), 5'ss of exon 2
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttgg--ttgtcatcattttatttataggtttttctttcttagatttgatgtttt-gtgtgggcag
|| |||||||||||||| || || || |||||||||||||| ||||| || |||||||| || |||||||| || ||||  ||||||||||||   | | | |||   |||||  || |||  |||  |    |  |   || ||    |  ||  ||||||| ||||  |   
GCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATTgtaagtatttt-tcactttttgtttggatttttcaggattccaaaattgtgaacttattgaaaattttgaatgtttttgtgttag---

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|110416715|gb|EC982713.1|EC982713
EST:     CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|110686941|gb|EE063919.1|EE063919
EST:     CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|32459229|gb|CD800403.1|CD800403
EST:     TCTGCAAGCAAAATATGTTGGAACTGGTCACATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: TCTGCAAGCAAAATATGTTGGAACTGGT--CATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|110687101|gb|EE064219.1|EE064219
EST:     CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|110394837|gb|EC960188.1|EC960188
EST:     CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|110731061|gb|EE108849.1|EE108849
EST:     CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|110419282|gb|EC985499.1|EC985499
EST:     CATCTGCATGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
EST: gi|110695800|gb|EE074233.1|EE074233
EST:     CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATT                         TGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA
genomic: CATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacc ... gtgtgggcagTGAATGGGCGGTGAATATCCAGCGTGATAGCTATGCATCATATGTTGGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTgtaagtaacctattattttagatttggttgtcatcattttatttataggtttttctttcttagatttgatgttttgtgtgggcag

- - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG