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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataatattcttatcaataaattcacattatttcttctcatcttatgtttttaagttgcgcatcagcctttggatgtatgttacataattaaacaa...

Basic information

species Vitis vinifera
transcript Vv09s0002g01630.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G40420.1 (Glycine max), 5'ss of exon 6
GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataatattcttatcaataaattcacattatttcttctcatcttatgtttttaagttgc--gcatcagcctttggatgtatgttacataattaaacaa--
||||||| |||||  |||| |||||||| ||||| || || || || ||||| |||| ||| |||||||| | |||||| || |||||||||||||||||||  || | ||  | || ||| | ||   |  | |||   |  | ||    | |||| |       || ||| ||    | |      ||| ||   | |   
GAGAAAGACAGGCTCACATAAACATTGCTGATGGAAAGAAGAGTTCAGTGATCTTAGCATCAGAAGCTGCGAGGATGGATCAAGTTAACAGAGCTCAAGgtta-attacatcttgataaattagtt---acaacttccagttgtgttgcaatattaattctttaagataagctttgatgtctgccgagcatgatgtgaaatcc

upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G14340.1 (Glycine max), 5'ss of exon 6
GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataatattcttatcaataaattcacattatttcttctcatcttatgtttttaagttgcgcatcagcctttggatgtatgtt--acataattaaacaa
||||||| |||||  |||| |||||||| ||||| || || || || || || |||| ||| ||||| |||| |||||| || |||||||||||||||||||  || | ||  | || ||| | |||  | |    |   |  | ||    | |||| ||    |       || ||||| || |   | | ||   | | 
GAGAAAGACAGGCTCACATAAACATTGCTGATGGAAAGAAGAGTTCAGTTATCTTAGCATCAGAAGCCGCAAGGATGGATCAAGTTAACAGAGCTCAAGgtta-attacatcatgataaattagttccaacttccaccagttgtgttgcaatattaattttttaagataagctttgatgtctgctgagcttgatgtgaaa-

upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT4G27585.1 (Arabidopsis thaliana), 5'ss of exon 6
GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat-attcttatcaataaattcacattatttcttctcatctta--tgtttttaagttgcgcatcagcctttggatgtatgttacataattaaacaa
||||||||||  |  | || |||||||| ||||| || ||||| || || || || | ||||||||| ||||||||||||||||| ||  |||| ||||||| |  |   |||   ||| | ||     ||   || | | | || |    ||||  | |||| | |   |       | |   | | |  |  |||     
GAGAAAGGCAATCCCATATCAACATTGCTGATGGTAAGAAAAGTTCTGTAATCTTGGCATCTGAAGCAGCAAAGATGGACCAGGTGAATCGAGCACAAGgttagtgagccattaagatcgagaacacatcagagttgcatgttatgtccattgttagttagtttcactagaagaaaaagttagttttcatttgcttatt---

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|18458599|gb|BM436877.1|BM436877
EST:     TAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: TAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
EST: gi|30324273|gb|CD007535.1|CD007535
EST:     GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
EST: gi|110377134|gb|EC942193.1|EC942193
EST:     GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
EST: gi|110393459|gb|EC958711.1|EC958711
EST:     GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
EST: gi|110385372|gb|EC949890.1|EC949890
EST:     GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
EST: gi|30325554|gb|CD008816.1|CD008816
EST:     GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
EST: gi|30327281|gb|CD010543.1|CD010543
EST:     GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAG                         GAGAAGCAGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG
genomic: GATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataat ... tatttttcagGAGAAGCGGAAGCCATTCTTGCTAGATCACAAGCAACAGCAAGAGGAATTG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAAGGCAGGCAAACATTAACATTGCAGATGGGAATAAAAGCTCCGTGATATTAGAATCTGAAGCTGCAAAGATGGACCAGGTTAACAGAGCTCAAGgttggataatattcttatcaataaattcacattatttcttctcatcttatgtttttaagttgcgcatcagcctttggatgtatgttacataattaaacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa