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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagttttttcatgctaactagacattggccttggttacctgattttaagctggatattgagttgaatgttacga...

Basic information

species Vitis vinifera
transcript Vv08s0007g01980.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 9
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagttttttcatgct--aactagacattggccttggttacctgattttaagctggatattgagttgaatgttacga
| |||||||| |||||||||||||| || ||  | || ||||| ||||| ||||| || || ||||| ||||||||||||||||||||||  ||      ||| || |     |  |     ||||   |  |||    |     | || |  | ||| ||||       || | |||| |       
TTAAAACAAACGATATGATGTTGGTCATATACTTGTCTTCTCTTATCCGGAGTGTCATCGCACTCCATAACTTGATCAATAACAAGgtaaattgtttctgtcttatctattgaatatagaagatgcgggagttaggagata---cttgtcattt-attgtaagacttccttttatttgattccag---

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 8
--------------TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaa------tatgccctcttctcata-tgaatgagtttttt----catgctaactagacattg--gccttggttac-ctgattttaagctggatattgagttgaa--tgttacga------------------------------------
              |||||||||| || ||||||||||| || ||||| || ||||| ||||| ||||| || || || ||||| |||||||| || |||||        | |  |  |||||  |  ||  | |||   ||    ||| |    ||||  |||  | ||| || ||  |||     ||      | | | |  |   || |  ||                                    
TTTCTTTTGTACAGTGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtttttatctgcttctggtgctgtttcagtcccttggtgcatcccttgtagattttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccag

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G368908_T03 (Zea mays), 5'ss of exon 6
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaa------tatgccctcttctcata-tgaatgagtttttt----catgctaactagacattg--gccttggttac-ctgattttaagctggatattgagttgaat--gttacga------------------------------------
|||||||||| || ||||||||||| || ||||| || ||||| ||||| ||||| || || || ||||| |||||||| || |||||        | |  |  |||||  |  ||  | |||   ||    ||| |    ||||  |||  | ||| || ||  |||     ||      | | | |  | |  | |  ||                                    
TGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAGgttggttgtttttatctgcttctggtgctgtttcagtcccttggtgcatcccttgtagattttgatgtctttgtgacattgaccactagtaatgaaatcactcaattttgctgtgagcatgaaatctggtctgttaattgctgtgattccag

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 9
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagttttttcatgcta-actagacattggccttggttacctgattttaagctggatattgagttgaatgttacga
||||||||||||| |||||| | ||||| ||||| ||||| ||||| || ||||| || || ||||||||||||||||| |||||||| | ||     |||  |            | | ||| |  | || | |   ||    ||   ||   || ||  | || ||  || |||  |        
TGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAGgttagatctttactttactc----------tctctcacggcacacaataatgtgattctga--actaaatcttgtgatg-atgctgtgtttcag-------

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 9
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagttttttcatgc---taactagacattggcct-tggttacctgattttaagctggatattgagttgaatgttacga
| ||||||||||| |||||| | || || || ||||| || || ||||||||||| || || |||||||  |||||||| |||||||||| ||   |  |  ||     | |    | |   | |    | | | ||  |||  || ||   |  |  ||||  | |      ||  |   ||||| |  
TAAAAACAAATGACATGATGCTCGTAATCTACCTTTCTTCGCTTATCCGAAGTGTAATCGCCCTCCACAGTTTGATCAACAACAAGgtaagatagaccatcatctctctatttctctctagtaggtgattgatttgaatttgctctatgcaaaatttgtttt--gttaatctgtggatgctatgtttcag

upper sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 5'ss of exon 9
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagtttt---ttcatgctaac-tagacattggccttggttacctgattttaagctggatattgagttgaatgttacga
|||||||||| || ||||||||||| ||||| || || || || || || |||||||| ||| | |||||| | || |||||||||||| || |   | |  | |        | || |   ||  |  | |  |||    ||   |  | ||  |   ||| ||| | ||||    |    | | ||  
TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAGgta-taagatttttgttgaggctgcccatttctaagtttttaatgatgtagctgatgatatacgctaattctcttttagc-gtatatca--tcagctatcactc

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|32459786|gb|CD800960.1|CD800960
EST:     CCACAACTTGAGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CCACAACTT--GATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110691663|gb|EE070021.1|EE070021
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|32245274|gb|CD711093.1|CD711093
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|33406522|gb|CF212149.1|CF212149
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110409702|gb|EC975372.1|EC975372
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110380658|gb|EC945941.1|EC945941
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|33406800|gb|CF212427.1|CF212427
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|26263205|gb|CA814268.1|CA814268
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110418075|gb|EC984190.1|EC984190
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110715119|gb|EE092808.1|EE092808
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|33409710|gb|CF215337.1|CF215337
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|32458047|gb|CD799221.1|CD799221
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTT
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|30296907|gb|CB973701.1|CB973701
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110409249|gb|EC974909.1|EC974909
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|30321841|gb|CD005103.1|CD005103
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGG
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGG
EST: gi|22008941|gb|BQ793975.1|BQ793975
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110387831|gb|EC952529.1|EC952529
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110380016|gb|EC945251.1|EC945251
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|45771085|gb|CN006937.1|CN006937
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|29783657|gb|CB349975.2|CB349975
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110732758|gb|EE108326.1|EE108326
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|30124736|gb|CB910075.1|CB910075
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|110396200|gb|EC961881.1|EC961881
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|33407874|gb|CF213501.1|CF213501
EST:     CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
genomic: CATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC
EST: gi|32457140|gb|CD798314.1|CD798314
EST:     TCTCTCATCCGAAGTGTTATAGCTCTCCACACAACTTGATCAATAACAAG                         ATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCTGCCGTC
genomic: TCTCTCATCCGAAGTGTTATAGCTCT-C-CACAACTTGATCAATAACAAGgtaatatgcc ... tggttttcagATGCTTAACAAAGAGCATGAGAAAGCTGAGGATGCAAAGCCAGCAGCCGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAGgtaatatgccctcttctcatatgaatgagttttttcatgctaactagacattggccttggttacctgattttaagctggatattgagttgaatgttacga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctt