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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGCGTGAGGTGGAAATATCTCATTGGGGCAGCATTCAGATCACAGAGCATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttctctgttatttggatatggtattgtcaatattgtccttcaaaatctatggaaagcatcttttcaagttaaggttttctgctattcagctgtt...

Basic information

species Vitis vinifera
transcript Vv13s0019g04410.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G35450.1 (Glycine max), 5'ss of exon 3
TTGTGCGTGAGGTGGAAATATCTCATTGGGGCAGCATTCAGATCACAGAGCATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaag---gttctctgttatttggatatggtattgtcaatattgtccttcaaaatctatggaaagcatcttttcaagttaaggttttctgctattcagctgtt
| |  |||||  | ||||||||||| ||||| ||||||||  |||| ||||| || |  ||||| ||||||||||| || ||||| ||  | |||||||||||     ||| |||  | |||   ||   |  ||       |   | |  |  ||| ||| ||  | | | |  |  ||      | | | ||| |   |  
TAGAACGTGAAATTGAAATATCTCACTGGGGAAGCATTCAAGTCACTGAGCAATATAGCTTGGTCCATGCTGGTGCTCGACATAAAGGTGTTTTTTCAAGgtatatttgttatctcctttttatttaacttgatgcttcagatcctcatttagttctttgggaaataacatgtgtaactattaaaat-tacaatttaaaag--
















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|161714140|gb|FC064411.1|FC064411
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|161714040|gb|FC064115.1|FC064115
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCCTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTAT
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTAT
EST: gi|351015486|gb|FQ447315.1|FQ447315
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|37187617|gb|CF606970.1|CF606970
EST:     CTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|349824067|gb|FQ417454.1|FQ417454
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|351031867|gb|FQ460124.1|FQ460124
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|352790365|gb|FQ478005.1|FQ478005
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|349812777|gb|FQ410419.1|FQ410419
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|349816667|gb|FQ404914.1|FQ404914
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|77585403|gb|DV221793.1|DV221793
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|161721124|gb|FC071011.1|FC071011
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCT
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCT
EST: gi|351051855|gb|FQ455269.1|FQ455269
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|351045790|gb|FQ440975.1|FQ440975
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTCCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|349811345|gb|FQ407571.1|FQ407571
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|351048526|gb|FQ448800.1|FQ448800
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|351053182|gb|FQ455639.1|FQ455639
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCGGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|349807244|gb|FQ401236.1|FQ401236
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
EST: gi|110414535|gb|EC980369.1|EC980369
EST:     CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAG                         GGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA
genomic: CATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttct ... tattttgcagGGTTGAATATCAGTCTAGACCATCTATCAGTGGTGTGTCTTCTTTCAAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGCGTGAGGTGGAAATATCTCATTGGGGCAGCATTCAGATCACAGAGCATTACAAGTTGGTTCATGCTGGTGCCCGGCATAAGGGAATCTTTTCAAGgtaaggttctctgttatttggatatggtattgtcaatattgtccttcaaaatctatggaaagcatcttttcaagttaaggttttctgctattcagctgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggaaa