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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT

Basic information

species Vitis vinifera
transcript Vv15s0046g02010.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 1
-------aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
       ||  |    |  |  ||   | ||| | ||    |||||| | |   |   | | || |  | |||    | ||      ||| |||| | |   |  ||||| ||  | ||||| ||||   | |||||||||||||| ||||||||||| |||||||| || ||    || |||||||| |||||| |  | ||||| 
gtgggggaaatgggtcacggcggcccaaaaatgttatg-gtttgactgcttgagtagatgtgatta-tattgtagtagtaat-----tttgtttttcctatttgtagCGCGGCTGTTAACTCGGAGAACGGCGAGGAAGTTGCCATCAAGAAGATTGGCAATGCATTCGACAACCATATCGATGCCAAGCGGACACTGAGAGAAATC

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G07270.1 (Glycine max), 3'ss of exon 1
----aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
            | ||| || |      | | ||| |  |||| |    | ||||||  | |||  | |||| | | ||   |  ||||||   ||||||||||||||||  | ||  |||||||| | |||||||||||||||||||||||||| |||||||||||||| || |||||||||||| |||| ||||| ||||||
ggtctgactaggagtaggagttcacttttgttatccatgtgacatagactttctgtt--agcaaggacgtgaggaacactattaattttttg--tttccttcagCGCTGCTGTAAATGCAGAGACAGGTGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTTGATAACAGAATAGATGCCAAAAGGACCTTACGAGAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 1
-aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
         | ||| || |      | ||||| |  |||| |   || |||| |     || |   ||   | ||||    |  |||||  ||||||||||||||||  | ||  |||||||| | |||||||||||||||||||||||||| |||||||| || || || |||||||||||| |||| ||||||||||||
ctgactaggagtaggagttcgtttttgtcatccatgtgacatagattttctgcta-gcaaaaaggatgtgaggaacactattaattttttgtttccttcagCGCTGCTGTAAATGCAGAGACAGGCGAGGAAGTTGCCATTAAGAAGATTGGCAATGCATTCGACAACAGAATAGATGCCAAAAGGACCTTACGGGAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 1
aagggcacaatagaagctacacaatttcatctaattgacttcatttct-ctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT-
||        |   ||  | |  |  |   || ||| |  |  |||    | | ||||||||||||||| ||| | ||||  ||||||   |||| ||||| |||||  | ||  |||||||||| || |||||||||||||||||| |||| ||||||||||| || || |||||||||||| ||||  |||| |||||| 
aaatttggtgtgttaggca-atgacctatactcattaatatggttttagttctgttatcaacaatgtgagggaca-atgttgttttttcattttctttcagtGCTGCTGTAAATGCAGAGACACGTGAAGAAGTTGCCATTAAGAAGGTTGGCAATGCATTTGACAACAGAATAGATGCCAAAAGGACTCTACGAGAAATTA

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 1
aagggcacaatagaagctacacaatttcatctaattgacttcatttctc--tgttttatcaacaatgtgaagga-aacatgtgttttttttcc--tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
          ||||   |      | |  ||| ||| |  | | ||     | | ||||||||||| ||| ||| ||  | | |||||| | |  |||||||||| |||||  | ||  ||||||| |  || |||||||||||||||||| |||| ||||||||||| || || |||||||||||| ||||  |||| ||||||
-----tgtgttagacaatgacttgtcttttctcattcatatgaatttagaatctgttatcaacaatatgagggacaatgttttttttttcttcaatttccttcagTGCTGCTGTAAATGCAGAGACGCATGAAGAAGTTGCCATTAAGAAGGTTGGCAATGCATTTGACAACAGAATAGATGCCAAAAGGACCCTACGAGAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G46070.1 (Arabidopsis thaliana), 3'ss of exon 1
aagggcacaatagaagctacacaat-ttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
          ||    ||    | | ||  ||| ||  | |         |   || |    |||||  |     || |  | ||  ||| |    ||||| |||||| ||||||||| |||  | ||| |||| || ||||||||||| |||||||| |||||||| |  || ||||| ||  | ||  |||| ||||||
---------gtaagttcttttgattctttgtctgataaattatgaaagcgttccttctattgaatgttca-----caggc-tcttgattcttgaatttcagTGCTGCGGTGAACTCAGTGACTGGAGAGAAAGTGGCTATTAAGAAGATCGGTAATGCTTTTGATAACATCATCGATGCTAAGAGAACGCTACGTGAAATT

upper sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 1
--aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgtt-ttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
    | |     | | | ||   | | || |||| || |  || |||      |  || |    |||   |       | |    ||| ||  | |  || || |||||   ||| || |||||  | |||||||| || || ||||||||||||||||||||||  || |  || || || ||  | || ||  | || |||
ttcggtgggtttttgtaactttgctactt-atctcatag--ttgattaagagatcattgtggtgaatagaagttttgaaggatcatttatttatctgatttagTGCTGCATGGAATTCGGAGACGGGTGAGGAAGTAGCGATCAAGAAGATTGGTAATGCATTTGGCAACATTATCGACGCTAAGAGAACTTTGAGAGAGATT

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|161717055|gb|FC068463.1|FC068463
EST:     TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|351036505|gb|FQ457218.1|FQ457218
EST:     GGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: GGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|110727011|gb|EE103312.1|EE103312
EST:     TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|110686022|gb|EE063251.1|EE063251
EST:     TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|351053736|gb|FQ441502.1|FQ441502
EST:     GGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: GGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|161706043|gb|FC054936.1|FC054936
EST:     TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGCGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|351046083|gb|FQ441466.1|FQ441466
EST:     GTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: GTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|352786392|gb|FQ479001.1|FQ479001
EST:     GGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: GGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|26261816|gb|CA812879.1|CA812879
EST:     TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: TACGTGCCGCCAATTCGGCCTGTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
EST: gi|351039574|gb|FQ461441.1|FQ461441
EST:     GTGGGTCGTGGTGCTTATGGTATCGTGTG                         CGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG
genomic: GTGGGTCGTGGTGCTTATGGTATCGTGTGgtaagaactg ... tttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT
                             catgtgttttttttcc  CT-rich tract
                                 tgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagggcacaatagaagctacacaatttcatctaattgacttcatttctctgttttatcaacaatgtgaaggaaacatgtgttttttttcctttccttcagCGCTGCGATGAACTCAGAGACACGGGAGGAAGTTGCCATTAAGAAGATTGGTAATGCATTTGATAATAGGATAGATGCCAAACGGACATTACGGGAAATT

- - - - aatagaa
- - - - - - - -gctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaca