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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactctctctctctctctctctctctcacacacacacacacacacacacaaagatgttgaaaattatagaagacagtttcttaagtaccacaaaattaagaaaatacttggttgtgaattgtgatttgcaaaaacattcttcaaatgattattggattgcag

Basic information

species Vitis vinifera
transcript Vv13s0019g04190.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 8
TGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgag------aactctctctctctctctctctctctcacacacacacacacacacacacaaagatgttgaaaattatagaagacagtttcttaagtaccacaaaattaagaaaatacttggttgtgaattgtgatttgcaaaaacattcttcaaatgattattggattgcag
 |||||||||||||||||||||||||| |||||| | || || || || ||||||||  |||| || || || || |||||||  || ||| | || ||||| ||      | |||| |   | | | | | | | | |          ||  ||||  |    | |||||  |  | | || | ||| | ||| | ||  |                                                                       
AGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGGTCGTCACATGCATTGCAAGAAATGTTCCTCGTgtaagtgttgaagctctatggttatttttatttgttttagttttgattgcat-cacatcctttaaggttgatcagca-acaacaaagtcttttagggacttc-----------------------------------------------------------------------

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G35560.1 (Glycine max), 5'ss of exon 8
TGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactctctctctctctctctctctctcacacacacacacacacacacacaaagatgttgaaaattatagaagacagtttcttaagtaccacaaaattaagaaaatacttggttgtgaattgtgatttgcaaaaacattcttcaaatgattattggattgcag
 ||||||||||||||||||||  ||||||||||||| || || ||||| || ||||||||||| ||||||||||| ||||||||||||||    |||||||| ||      |||  ||| ||||| |    |||| | |      ||      |||  |   |  |  ||  | |  | | ||    |||||  |  || |  |                                                               
GGAATATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTAACATGCATTGTGAGGAACTGTCCACGTgtaag----tcctccatctgtctctattaagcacaaataattgggcaagatagcaagtagagtttaggttgcaaatta-aattataaaagtaatagcaactgcaa--------------------------------------------------------------

upper sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 8
TGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactctctctctctctctctctctctcacacacacacacacacacacacaaagatgttgaaaattatagaagacagtttcttaagtaccacaaaattaagaaaatacttggttgtgaattgtgatttgcaaaaacattcttcaaatgattattggattgcag
 || |||||||||||||||||  ||||||||||||| || || ||||| || ||||||||||| |||||||| || ||||||||||||||    ||||| || ||   ||| ||  | |  |||| |    |||| | |      ||      |||  |   |  |  ||  | |  | | ||    ||||   |  || |  |                                                               
GGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTGTTGTGACATGCATTGTGAGGAACTGTCCACGAgtaag---tctttccatatgcctctattaagcacaaataattgggcaagatagcaagtagagtttaggtttcaaatta-aattataaaagtgataacaactgca---------------------------------------------------------------

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|110372418|gb|EC936581.1|EC936581
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|30326726|gb|CD009988.1|CD009988
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|156737328|gb|EV241442.1|EV241442
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|32249612|gb|CD715431.1|CD715431
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|32247169|gb|CD712988.1|CD712988
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|110395213|gb|EC960849.1|EC960849
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|29783210|gb|CB349240.2|CB349240
EST:     GGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|30325548|gb|CD008810.1|CD008810
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|110703011|gb|EE079483.1|EE079483
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGA--AATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|32248621|gb|CD714440.1|CD714440
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|156737322|gb|EV241443.1|EV241443
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
EST: gi|30324763|gb|CD008025.1|CD008025
EST:     GAGATTCTGTTGGTGGTGTTGTAACTTGCATTGTGAGGAATGTCCCACGT                         GGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT
genomic: GAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactc ... tggattgcagGGCCTTGGATCACCAGTCTTTGATAAACTTGAAGCTGAGTTGGCTAAAGCT

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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTGTTGTAACTTGCATTGTGAGGAATATCCCACGTgtgagaactctctctctctctctctctctctcacacacacacacacacacacacaaagatgttgaaaattatagaagacagtttcttaagtaccacaaaattaagaaaatacttggttgtgaattgtgatttgcaaaaacattcttcaaatgattattggattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG