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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagctattatttggttggtgtttagtttttcctttatgctattgggttcttcagttgttttgcttttcatctcatgtgttgtgctggtgttacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG

Basic information

species Vitis vinifera
transcript Vv17s0000g08930.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------------------gagctattatttggttggtgtttagtttttcct--ttatgctattgggttcttcagttgttttgcttttcatctc-atgtgttgtgctg-gtgttacactg--cagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG
                                                                                              |   | || |||  |  |   || ||| ||| |  ||||  |    |  |  | | || |   |  || ||| ||      || || |  ||||     ||   ||||||| ||||||||||||||||||| |||| | ||||| |||||||||||||||||||| || ||||| || ||||| |||||||||
gtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttattatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------------------------------------gagctattatttgg---ttggtgtttagt-ttttcctttatgctattgggttcttcagttgttttgcttttcatctcatgtgttgtgctggtgttacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG
                                                                                                      || | || ||    ||| | || |   || | |  | |  ||||   ||     | |    |  | |    || |||| |||||   |  |     |  ||||||| ||||||||||||||||||| |||| | ||||| |||||||||||||||||||| || ||||| || ||||| |||||||||
gtaaactttctatattcagtatggcattgtttcacagtttgattagttttattctgccaaatcacattgaaggttgcctaatctgaccatttctctatttttctttcatatgaaatttgttattcatcattattccctgtcgtattatttttgaaggcttgcataatctgacccttatgttttgtgtctgcttg----tttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------gagctattatttggttg-----gtgtttagtttttcctttatgctattgggttcttcagttgttt--tgcttt-----tcatctcatgtgttgtgctggtgttac-actgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG
                                     || |  |  |   ||||     |||||||| ||||   |  |  | ||| ||  | |  | | ||  ||||||     |||    |  ||   |     ||  ||   |||||||||||| | |||||||| |||| | ||| || || ||||| ||||||||||||||||| |||| ||| |||||||| || || |||
gtacagtattccaagacctatcctgctaatattttatgaacattagtgaagttgcaattgtgtttaggttttgagtagtatttttgcgtcataccttagattaatgctttcgcagtcactgtacatgccctaacattgcaactgttgcagTTTGGAAAACAAAGTCATCCAGAGTGTGCACGATTCTCTCCCGATGGGCAGTTTCTTGTTTCTTCCTCAGTGGATGGCTTCATCGAG

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|33403436|gb|CF209063.1|CF209063
EST:     AACAAGATGTAGATGATATGTATCGATCAACTCTCGGGCACACCATCAAG                         TTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAG
genomic: AACAAGATGTAGATGATATGTATCCAACAACTCTCGGGCACACCATCAAGgtaaggtgta ... tacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAG
EST: gi|71862424|gb|DT011479.1|DT011479
EST:     AACAAGATGTAGATGATGTGTATCCAACAACTCTCGGGCACACCATCAAG                         TTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAG
genomic: AACAAGATGTAGATGATATGTATCCAACAACTCTCGGGCACACCATCAAGgtaaggtgta ... tacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAG
EST: gi|30129597|gb|CB914936.1|CB914936
EST:     AACAAGATGTAGATGATATGTATCCAACAACTCTCGGGCACACCATCAAG                         TTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAG
genomic: AACAAGATGTAGATGATATGTATCCAACAACTCTCGGGCACACCATCAAGgtaaggtgta ... tacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttcagttgttttgcttttcatctcatgtgttgtgctggtgttacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG
         ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagctattatttggttggtgtttagtttttcctttatgctattgggttcttcagttgttttgcttttcatctcatgtgttgtgctggtgttacactgcagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - -tggttgg
- - - - - - - - - - - - - - - - - - - ctattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctgg