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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttacattttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag

Basic information

species Vitis vinifera
transcript Vv18s0072g00720.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G044681_T01 (Zea mays), 5'ss of exon 5
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGT-TTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttacat-tttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
 ||||| ||||||||| |||| ||| ||||||||| || | || |  ||   | | ||   | |||| |||||||| |||||||||||||||||||| |||||        |   | | | | ||  |  ||  | |    || |    | |  |||  |    || |||| |  |  | || ||                                              
GGAAGATCCTGAAGGTGCAGGTACTGCTCACTTGTATTCAGTG-ACACAAAAAATTAGTGGTGTGGCGAATCGTGCATTTGAGCCTCTATTTGAGAGGCAGgtatagaaactgagcttctctagaactactgctatt----gcttcaacattccttgagtgcactg-aattctgaacttctggtacag-------------------------------------------

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G050647_T01 (Zea mays), 5'ss of exon 5
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGT-TTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttaca--ttttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
 ||||| ||||||||| |||| ||| ||||||||| || | || |  ||   | | |||  | |||| |||||||| |||||||||||||||||||| |||||   |    |   |    | | ||  | |||  | | |   |  ||||  || |||  |    |  |||| |  |  | || ||                                              
GGAAGATCCTGAAGGTGCAGGTACTGCTCACTTGTATTCAGTG-ACACAAAAAATTAGCGGTGTGGCAAATCGTGCATTTGAGCCTCTATTTGAGAGGCAGgtatataaactaagctgtctctagaactattgctattgctt-caagtttccttattgagtgcacta-aattcttaacttctggtacag-------------------------------------------

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AC194296.3_FGT001 (Zea mays), 5'ss of exon 10
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttac--attttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
                                        || |  |    | | ||   | |||| |||||||| |||||||||||||||||||| |||||   |    |   |    | | ||  | |||  | | |   |  ||||  || |||  |    |  |||| |  |  | || ||                                              
----------------------------------------TG-ACACTAAAAATTAGTGGTGTGGCAAATCGTGCATTTGAGCCTCTATTTGAGAGGCAGgtatatacactaagctgtctctagaactattgctattgctt-caagtttccttattgagtgcacta-aattcttaacttctggtacag-------------------------------------------

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G31490.2 (Glycine max), 5'ss of exon 5
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttacattttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
 || ||||||||||| || || ||||| || |||||||||  |||||||| ||| || |  | ||||||||||||| |  ||||| |||||||||||||||| | ||   | |  ||| | |||||  | |  |       ||| |  |||   |  ||     ||||| |||  ||    | | || ||    | |                                
GGATGACCCTGAAGGGTCTGGGACTTCCCATTTGTTTAATATTATTCAGGAAGTTAGTTTGCAGGCTAATCGTGCCCTGAAGCCTTTATTTGAGAGACAGgtggctgaagtatttattctagattttgttgcgg-------ctgct--attccagatttcaaaataattttattcatgacttctatgaattgtgtag--------------------------------

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G36120.1 (Glycine max), 5'ss of exon 5
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggt--gtgatttacattttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
 || ||||||||||| || || ||||| || |||||||||  ||||||||  || || |  | |||||||||||||||  ||||| |||||||||||||||| ||   |||  | |  | ||   | |       |||  ||| || |  ||| | |  ||     ||||| |||  |     | | || ||    | |                                
GGATGACCCTGAAGGGTCTGGGACTTCCCATTTGTTTAATATTATTCAGGATGTTAGTTTGCAGGCTAATCGTGCCTTGAAGCCTTTATTTGAGAGACAGgtgggctggtggctgaagtctttattctagattttgttgtggc-tgct--attctagatttcaaaataattttattcacgacttctatgaattgtgtag--------------------------------

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G76850.1 (Arabidopsis thaliana), 5'ss of exon 5
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttacattt--tggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
||||||||| ||||||||||||||| |||| ||||||||||||||  |  | || |  ||   ||| |||| ||| |||||||| || ||||||||||||||||||||||||   ||||  |   |||| | |    ||       |||   ||  |  ||| |   |||   ||  |                                                     
AGAAGACCCCGAAGGTTCAGGAACTACTCATTTGTTTAATTGTATGAAAAGTGTGACATCGAGGGCCAATCTTGCATTTGAGCCACTTTTTGAGAGACAGgttggtgtgattctgatttacttcttttgcttgtcactctctttcattttgctgaagcctttttcaaaatcacatttag----------------------------------------------------

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G21170.1 (Arabidopsis thaliana), 5'ss of exon 5
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatt-tacattttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagat-atgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag
||| ||||| || || || |||||| |||| ||||||||||||||  || | || |  || | |||||||||||| |||||||| || ||||||||||||||| || || |     | | | | ||| ||||   ||    |||      ||| |  || || |   | ||| |  |  ||  |   | |                                         
AGACGACCCAGACGGATCGGGAACTACTCATTTGTTTAATTGTATGAAGAGTGTGACATCACGGGCTAATCGTGCTTTTGAGCCACTTTTTGAGAGACAGgtttgtatggtcacgtactattgtttttttggtgtttt---cctagcctcttgct--atctgcttagactgttttcaccattattcatag-----------------------------------------

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|30327435|gb|CD010697.1|CD010697
EST:     GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAG                         GCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTT
genomic: GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtga ... gctgttgtagGCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTT
EST: gi|32248056|gb|CD713875.1|CD713875
EST:     GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAG                         GCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCAAAGATTCCGA
genomic: GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtga ... gctgttgtagGCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCAAAGATTCCGA
EST: gi|32272073|gb|CD721232.1|CD721232
EST:     GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAG                         GCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCANAGATTCCGA
genomic: GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtga ... gctgttgtagGCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCAAAGATTCCGA
EST: gi|32272496|gb|CD721655.1|CD721655
EST:     GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAG                         GCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCNAAGATTCCGA
genomic: GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtga ... gctgttgtagGCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCAAAGATTCCGA
EST: gi|32248851|gb|CD714670.1|CD714670
EST:     GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAG                         GCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCANAGATTCCGA
genomic: GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtga ... gctgttgtagGCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCAAAGATTCCGA
EST: gi|32249201|gb|CD715020.1|CD715020
EST:     GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAG                         GCTCANACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCANAGATTCCGA
genomic: GAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtga ... gctgttgtagGCTCAAACTGAGAAGATCAGATCTGTGCAAGGAATGCTTCAAAGATTCCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGACCCTGAAGGTTCAGGAACTTCTCACTTGTTTAATTGTATTCAGGGAGTCAGCTCTCTGGCTAATCGTGCCTTTGAGCCTCTATTTGAGAGACAGgttggtgtgatttacattttggatttgttggaagttcaggcctgtttaattgttggatttgttgtaattgtatagatatgctatgtggatcaatttgtttcatttattttttcaacaatgctgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC