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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGACACATACTTGATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatgacgctttaacttgataaatgcttggtgaaatttgatagcagaagccaactaaatattttctccacatgaatgatggaaaattcacatcttcgcctagtgtgttccagataatttattcttgtttcctgtcttcttcctgtgttaagatttaactaattctatag

Basic information

species Vitis vinifera
transcript Vv06s0004g02820.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G179732_T03 (Zea mays), 5'ss of exon 2
GTTGACACATACTTGATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatgacgctttaacttgataaatgcttggtgaaatttgatagcagaagccaactaaatattttctccacatgaatgatggaaaattcacatcttcgcctagtgtgttccagataatttattcttgtttcctgtcttcttcctgtgttaagatttaactaattctatag
|   | |||||  |||  |||||||||||   |||||||||||| ||| |||||||||||| ||||| | | |    |||   |  |||  || || ||||    || |||  ||  ||    || ||| | | |  | ||  |||      ||| | ||||     | || | | ||    | ||| | |                                                
GAACATACATATGTGACTTTGCTTACTACACGATCAGATGCTTTTTATGATCTCAAAGATTCCAGgtgagcta----gctaataaatgactaa-gcatggt----ttggatgtcacgaggtgtctgaatgtgtgccac-caaaaat------aaactgacata---acttattcttttgtgaacaatgtctag----------------------------------------------

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA12G29450.3 (Glycine max), 5'ss of exon 10
GTTGACACATACTTGATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatgacgctttaacttgataaatgct--tggtgaaatt-tgatagcagaagccaactaaatattttctccacatgaatgatggaaaattcacatcttcgcctagtgtgttccagataatttattcttgtttcctgtctt-cttcctgtgttaagat----ttaactaattctatag
| ||||||||||||||||||||| || || |  || ||||| || |||||||| || |||||||||||||  |||      |||  |||    || |  |  ||   |  ||||     |        |||            | ||   | | | |       || | ||  || |     |||    | | |     | || |   |  || | ||  | |  ||    ||  | ||||| | ||
GATGACACATACTTGATGTTGCTGACCACAAGTTCTGATGCATTTTATCATCTTAAGGATTGCAGgtaaatgatggtttaataatctgactgctgttattattgggttcatgatgttttatttgggagaaaagaagaaaattaaagaggaaagaacataatgattcatagcaaagagatcctcagtctctatgtagcaatatctttcttggctgcatggttcagaatcttgtttgccaattc-acag

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA13G40080.1 (Glycine max), 5'ss of exon 11
GTTGACACATACTTGATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatgacgctttaacttgataaatgct-tggtgaaatt--tgatagcagaagcca-actaaatattttctccacatgaatgatggaaaattcacatcttcgcctagtgtgttccagataatttattcttgtttcctgtctt--cttcctgtgttaagat----ttaactaattctatag
| ||||||||||||||||||||| || ||||  || ||||| || || ||||| || |||||||||||||  |||      |||  |||    || | | ||    ||  ||||     |      |  ||| |        | |     ||  ||| ||    ||      | |     | |    |   |   |     |  || ||||  || | ||  | |  ||    ||  | ||||| | ||
GATGACACATACTTGATGTTGCTGACCACTAGTTCTGATGCATTTTACCATCTTAAGGATTGCAGgtaaatgatggtttaataatctgactgctgttattgttgggttcatgatgttttatttgggagaaaagaagaaaattaaaaaggggagagaacataatgattcatagcaaagagatcctcagtctctacgtagcaatatctttcttggctgcttggttcagaatcttgtttgccaattc-acag

upper sequence: Vv06s0004g02820.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGACACATACTTGATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatgacgcttta-acttgataaatgcttggtgaaatttgatagcagaagccaactaaatattttctccacatgaatgatggaaaattcacatcttcgcctagtgtgttccagataatttattcttgtttcctgtcttcttcctgtgttaagatttaactaattctatag
| ||| |||||  | || |||||||| ||    |||||||| ||| |||||||||||||||||||||||   | |     | | |||||| |  | || |      ||| | |  ||||      |||| ||   |     ||  |       ||| |   |  |  |  |||                                                                   
GATGATACATATGTAATATTGCTTACCACACGTTCAGATGCGTTCCATCATCTCAAAGATTGCAGgtaataaaagctatatcatacttga-aggtactcgt--gttttttacatgagaaaatgcttaaa-ataagcatgttattgagttccataaacttgtacat--ggttag-------------------------------------------------------------------

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|110360647|gb|EC923921.1|EC923921
EST:     CAAAGATTGCAG                         GCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
genomic: CAAAGATTGCAGgtaaaccatg ... aattctatagGCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
EST: gi|22014663|gb|BQ799697.1|BQ799697
EST:     ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAG                         GCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
genomic: ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatg ... aattctatagGCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
EST: gi|33403777|gb|CF209404.1|CF209404
EST:     ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAG                         GCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
genomic: ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatg ... aattctatagGCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
EST: gi|22014543|gb|BQ799577.1|BQ799577
EST:     ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAG                         GCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
genomic: ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatg ... aattctatagGCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
EST: gi|110412539|gb|EC978290.1|EC978290
EST:     ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAG                         GCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
genomic: ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatg ... aattctatagGCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA
EST: gi|33403454|gb|CF209081.1|CF209081
EST:     ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAG                         GCTTCGTATTGAGACGGAGCTTTTGAAGTCAAATGTTCTCAGCGAAGATCA
genomic: ATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatg ... aattctatagGCTTCGTATTGAGACGGTGCTTTTGAAGTCAAATGTTCTCAGCGAAGTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGACACATACTTGATGTTGCTTACTACTAAATCAGATGCTTTCTATCATCTCAAAGATTGCAGgtaaaccatgacgctttaacttgataaatgcttggtgaaatttgatagcagaagccaactaaatattttctccacatgaatgatggaaaattcacatcttcgcctagtgtgttccagataatttattcttgtttcctgtcttcttcctgtgttaagatttaactaattctatag

- - - - - - - - - - - - - - - - - CAGATG