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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgtatgagatgaccatttattacag

Basic information

species Vitis vinifera
transcript Vv04s0008g04690.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataa--ctattgt-atgagatgaccatttattacag
 ||||| ||||||||||| || ||||| |||||||| |||||||| ||| | |||||||| || ||||| ||||| |||||||| |||||||| || |||||   ||      | | || | | |  ||  || ||     ||  |  | || ||  |   |||||| |   | | |   ||   | |||
GATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTCCAGCGAACCATGCTTGAGCTTCTGAACCAACTTGATGGTTTTGAAGCATCAAACAAAATAAAGgtgtgcc------actgctttgcatatgttatatgtgccgattaataaccgtgaaggagtttattgtgacacgttaaatgttccatgcag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G137528_T01 (Zea mays), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttggtagtaagtta--aattttgtctctgtaaataactattgt-atgagatgaccatttattacag
|||||| ||||||||||| || |||||||||||||||||||| || ||| | || ||||| || || || ||||| |||||||| |||||||| || ||||||| |   ||| | || | ||| || |   | | |||   ||||    |   |  ||||| || || |||   | |  ||||| | |||
AATGGAGTCTGGAACTGGCAACGGTGATAGTGAAGTGCAGCGTACCATGCTTGAACTTCTAAACCAGCTTGATGGTTTTGAAGCTTCAAACAAAATTAAGgtacac---aatcacttgtgttcctttgcgatgaattagtgatttgtaataaatgtataacaatcgtgatgttttaaatatttaatgcag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G107362_T04 (Zea mays), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgt-atgagatgaccatttattacag
|||||| ||||||||||| || ||||| |||||||| ||||| |||||| | || ||||| || || || ||||| |||||||| |||||||| || ||||||| | ||| |  |    ||  ||      | ||| |   |||||   ||||  ||||  || | |||   |||  ||||| | |||
AATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGTACTATGCTTGAACTTCTAAACCAGCTCGATGGTTTTGAAGCATCAAACAAAATTAAGgtacacatcacttgtgctcctgtgtgctggattagtga---tttgtaaatgta--taacagttatgatgttttgaatatttaatgcag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G24000.1 (Glycine max), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctct-tcgttggtagtaagttaaattttgtctctg--taaataactattgtatgagatgaccatttattacag----------------------------------------------------------------------------------------------
 ||||||||||||| ||| |||||||||||||| || ||||| |||||| |||| |||||||||||  |||||||||||||||| ||||||||||||||||||      |  |  |   || |  |  ||| ||||   ||||||    ||      ||  | | |||     |     || | | ||||                                                                                              
GATGGAATCTGGAAGTGGCAATGGTGATAGTGAGGTACAGCGTACTATGCTGGAACTTCTCAATCAGTTGGATGGATTTGAAGCTTCAAACAAGATCAAGgtaa-----aggagctatactgttatgtgtattaaggggaattttaaagctagtcttatgtccactgttctgaaaagaaatctgtaacagttgaacttaacagatattatttactctgtctgactcatttgagatgagttctcaattctttgtggaggttctgaagataaattttcaattgtag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G00420.1 (Glycine max), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttgg--tagtaagttaaattttgtctctg--taaataactattgtatgagatgaccatttattacag-------------------------------------------------------
 ||||||||||||| ||| || ||||||||||| || ||||| |||||| |||| |||||||| ||  |||||||||||||||| ||||| ||||||||||||      |  |  |   ||    | |  || ||||   ||||||    ||      ||  | | |||   | |     || | | ||||                                                       
GATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGTACTATGCTGGAACTTCTCAACCAGTTGGATGGATTTGAAGCTTCAAATAAGATCAAGgtaa-----aggagctatactgtaatagtgtattaaggggaattttaaagctagtctgatgtccactgttctaaaaagaaatatgtaacagttgaacttaacagatattatttaccctctcatttgagaaaaattttcaattgtag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaa-taatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgtatgagatgaccatttattacag-----------------------
 ||||||||||||| |||||||||||| ||||| ||||| || || ||| | ||||||||||||||||| || || |||||||| |||||||| ||||||||||   | || |  |                |||||| |||    |   | |   | | | | || ||| ||  |         ||                        
TATGGAATCTGGAAGTGGAAATGGTGACAGTGAGGTGCAACGGACCATGCTCGAGCTTCTCAATCAACTTGACGGTTTTGAAGCGTCAAACAAAATCAAGgtacctattaagttgtaaaggaaaaaaaaccataagttgaataggatgagtctgtgttattgtagtctgaaattgctgacagagtcatattctctttaatgactgttgcag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca-----------ataatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgtatgagatgaccatttattacag-------------
 ||||||||||| | |||||||||||| ||||| |||||  | |||||| | ||||||||||||||||| || ||||| || || |||||||| |||||||||  ||| |           | ||  |      |  | |   |||   || | ||| |   |    |  |     |  |  |    | || |   |              
TATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGGACTATGCTTGAGCTTCTCAATCAACTTGACGGATTCGAGGCGTCAAACAAAATCAAGgtatgccttatgttgtgaatgaaaaaatagtcatgaagctgaaaaggataactctgtgttactctgaatttcgcagacaaagttgttaattctcttaaatgactgttgcag

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 5'ss of exon 1
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtac----tcctcaataatttctcttcgttgg-----tagtaagttaaattttgtctctgtaaataactattgtatgag-atgaccatttattacag---
  | || ||||| | ||| ||||| ||||||||||| || || || ||||||||| |  | ||||||||||||||||||||||| || |||||||||||||||     |    |  |||| |  |    | |     |  |      |  | ||||    |   |   || | | |||| ||||    |    |||    
TGTCGAGTCTGGGAATGGTAATGGAGATAGTGAAGTCCAACGGACAATGTTGGAGTTGTTGAATCAACTGGATGGATTTGAAGCATCTAACAAGATCAAGgtaaattatttctatcaattacattgtaatcgacttttgttcgaccgagctgtgtcatgttgtgtttgtactttgtgaggatgaatcctaccgacactgt

upper sequence: Vv04s0008g04690.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 5'ss of exon 6
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgt--actcctcaataatttctct-tcgttggtagtaagttaaattttgtctctgtaaataactattgtatgagatgac-catttattacag------------------------------------------------------------------------
  |||| ||||| | ||| ||||| ||||||||||| ||||| || ||||||||| |  | ||||| || ||||| |||||||| || |||||||| |||||   ||| |||  | |  | |  | |  |  | | | |||  | ||     |||   |    ||| |||||     |  | ||   | ||                                                                        
TGTGGAGTCTGGGAATGGCAATGGAGATAGTGAAGTTCAGCGGACAATGTTGGAGTTGTTGAATCAGCTTGATGGGTTTGAAGCGTCGAACAAGATTAAGgtttgctcttcacaactgacacaattgaggtcatttacttatttgtttgagttgtttgtggtaattctatgatccttcatacttgaaaaagggtctcatcaatcttgctatttgccagcttagctcgaattgttcgttaactcacattgttgtaacattgtag

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|161719441|gb|FC067675.1|FC067675
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110693738|gb|EE070234.1|EE070234
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|83275357|gb|DV939365.1|DV939365
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110369927|gb|EC934100.1|EC934100
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110393851|gb|EC959383.1|EC959383
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110716592|gb|EE091708.1|EE091708
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110413978|gb|EC979798.1|EC979798
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|56409639|gb|CX017891.1|CX017891
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|83275019|gb|DV939115.1|DV939115
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|56409619|gb|CX017871.1|CX017871
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|22011936|gb|BQ796970.1|BQ796970
EST:     GATGGA-TTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: GATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110391091|gb|EC956045.1|EC956045
EST:     TGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110403181|gb|EC964466.1|EC964466
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|349826120|gb|FQ415925.1|FQ415925
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|30302866|gb|CB979660.1|CB979660
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110686251|gb|EE063682.1|EE063682
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110703733|gb|EE080835.1|EE080835
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110724539|gb|EE100454.1|EE100454
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|110414055|gb|EC979878.1|EC979878
EST:     GCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: GCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
EST: gi|30302923|gb|CB979717.1|CB979717
EST:     TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAG                         GTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG
genomic: TGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctca ... tttattacagGTTTTGATGGCTACAAATCGCATTGATATTTTGGATCAAGCCCTCCTTAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAATCTGGAACTGGAAATGGTGATAGTGAAGTGCAGCGAACTATGTTGGAGCTTCTCAATCAACTGGATGGATTTGAAGCCTCAAACAAGATCAAGgtactcctcaataatttctcttcgttggtagtaagttaaattttgtctctgtaaataactattgtatgagatgaccatttattacag

- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA