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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaaaaaataatttgccacagaaaaatatctgatgctatttggtgcaatttcctatgtcacaacttgagagtgtttaatgtctactgctttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGGTTTCTGGGACCGCGCGGAAGTATTACATGCTAGGTGGGAAGGGTGGTGT

Basic information

species Vitis vinifera
transcript Vv13s0019g04590.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 1
-----cttcaaaaaataatttgccacagaaaaatatctgatgctatttggtgcaatttcctatgtcacaacttgagagtgtttaatgtctactgctttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGGTTTCTGGGACCGCGCGGAAGTATTACATGCTAGGTGGGAAGGGTGGTGT
      ||    |   ||||||        |    | |||  | || |  || | | |   ||  ||||  ||   | || ||| || ||  |  |  ||| ||||||||||| | |||| | || |||||||||   | ||||||||||||||||||||||||||   | ||||||||||||||||||||||||| || || ||
gatgcttttcttaggcaatttgtgcttttga--cttttgagac-atctattg-agtatttaataacacattttttta-tggttattgcctttttttaattgtcagTGAGATCAATTGCTGGTACTACAGAAGCTGCATCGGGGTTTGATGAGATGGTTTCTGGGACTAAGAGGAAGTATTACATGCTAGGTGGGAAAGGGGGAGT

upper sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G35320.1 (Glycine max), 3'ss of exon 1
-----cttcaaaaaataatttgccacagaaaaatatctgatgctatttggtgcaatttcctatgtcacaacttgagagtgtttaatgtctactgctttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGGTTTCTGGGACCGCGCGGAAGTATTACATGCTAGGTGGGAAGGGTGGTGT
      |  |      ||||||        |  | |  || |   ||||    | |||   ||  |||   ||     || ||| |  ||  |  |  ||| ||||||||||||| |||| | || |||||||||   | ||||||||||||||| ||||||||||   | |||||||||||||||| |||||||| || || ||
tttttttataggcggaaatttgtgcttttgagttttgagacgtcttttg----agtttttgataacactttttttttatggttattacctttt-ttaattgtcagTGAGATCAGTTGCTGGTACTACAGAAGCTGCATCGGGGTTTGATGAGATGATTTCTGGGACTAAGAGGAAGTATTACATGCTTGGTGGGAAAGGGGGAGT
















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|351013747|gb|FQ433899.1|FQ433899
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|352790386|gb|FQ478026.1|FQ478026
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCCGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|294965156|gb|GW836987.1|GW836987
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGTTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|351028016|gb|FQ425917.1|FQ425917
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|349820813|gb|FQ404198.1|FQ404198
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|349812310|gb|FQ406331.1|FQ406331
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|161720443|gb|FC070210.1|FC070210
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|26257255|gb|CA808318.1|CA808318
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|349817149|gb|FQ405154.1|FQ405154
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|349827879|gb|FQ422747.1|FQ422747
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|26257525|gb|CA808588.1|CA808588
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|351025874|gb|FQ427886.1|FQ427886
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|351029701|gb|FQ427541.1|FQ427541
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
EST: gi|71861294|gb|DT010349.1|DT010349
EST:     TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAG                         TGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG
genomic: TTTTCTCCCTGTCAGAGTCACAAGAAAACCACCAAGGAAATCACTTCAAGgtgaaatatt ... tttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaatttcctatgtcacaacttgagagtgtttaatgtctactgctttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGGTTTCTGGGACCGCGCGGAAGTATTACATGCTAGGTGGGAAGGGTGGTGT
                             gtttaat  putative branch site (score: 4)
                                         ctgcttttt  putative PPT
                            tgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcaaaaaataatttgccacagaaaaatatctgatgctatttggtgcaatttcctatgtcacaacttgagagtgtttaatgtctactgctttttggcagTGAGATCAGTGGCTGCTCCTTCAGAAGCTGTTGCTGGGTTTGATGAGATGGTTTCTGGGACCGCGCGGAAGTATTACATGCTAGGTGGGAAGGGTGGTGT

- - aaaaaat
- - -aaaaata
- - - - - - - -tgccaca
- - - - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - tggtgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctactgc