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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatatctggatttcgtacttttgaaacatgtgatcatttcaaaatcaactgatgaaaacagtacatttctt...

Basic information

species Vitis vinifera
transcript Vv05s0102g01180.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA13G42070.2 (Glycine max), 5'ss of exon 4
GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatat-ctggatttcgta--cttttgaaacatgtgatcatttcaaaatcaactgatgaaaacagtacatttctt-----------------
||  | |||||||| ||||||||    ||||| |||||||| |||||||||||||| ||||||||||||  |||||| || || |||||||||||||||||||| |||    | ||| |   ||||| || | | ||  || | |||   | || ||| |     |  | |         || ||      |||    |  ||                 
GAAAGGATTCCTGGCATTGATATCCACTTGAATGATGGAGATAAGTGGATGTTTGCTGGCCATGAGGTGCGTGTAATGGACACGCCTGGTCATACCCGAGgtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcag

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA15G03320.1 (Glycine max), 5'ss of exon 4
GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatat-ctggatttcgta---cttttgaaacatgtgatcatttcaaaatcaactgatgaaaacagtacatttctt-----------------
 |  | |||||||| ||||||||    ||||| ||||| || |||||||||||||| ||||||||||||  |||||| || ||||||||||| |||| |||||| |||    | ||| |   ||||| || | | ||  || | |||     ||  ||| || || |   ||  |  |   || ||      |||    |  ||                 
AAAAGGATTCCTGGCATTGATATCCACTTGAACGATGGTGATAAGTGGATGTTTGCTGGCCATGAGGTGCGTGTAATGGACACTCCTGGTCACACCCAAGgtcacattcatgctctatttgcattagtaattcttcttaatattgtaaagtattaaaaaaatctggtttcttttatgt-ggctcatttttctagtgttctatttatttatactgtatgcag

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G43430.2 (Arabidopsis thaliana), 5'ss of exon 3
GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatatctggatttcgtacttt---tgaaacatgtgatcatttcaaaatcaactgatgaaaacagtacatttctt
||||| |||||||||||||| ||| || |||| ||| | || |||||||||||||| |||||||||||     || |||| |||||||| ||||| | ||||          ||  |    || |  ||||||    ||   | |   |    | ||| || ||   |  | | || |   || || |      | |||  | 
GATCGGATTCCTGGAATTGACATACTTCTGAAGGATAGTGATAAGTGGATGTTTGCTGGCCATGAGGTTCGGATACTTGACACTCCTGGCCATACACAAGgtttgtagctgccataacctctactgtaaaatactaagaacacatctatacagtcaaatat-tgccaacgttagaaacctttggtgga--tcacatattagta

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G06130.2 (Arabidopsis thaliana), 5'ss of exon 4
GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatatctggatttc-gtacttttgaaacatgtgatcatttcaaaatcaactgatgaa-aacagtacatttctt
|| || ||||||||||||||| |||  ||||||||||  ||||| ||||||||||| |||||||| ||   | | || ||||||||||| || ||| |||||   ||    |  | |     | | || | | | |   |||| ||  ||     | ||        |||| | |      | |   |    | || | | |
GACCGGATTCCTGGAATTGATGTAGCCTTGAAAGATGCTGACAAATGGATGTTTGCTGGCCATGAAGTCCATATTATGGAAACTCCTGGCCACACCAGAGgttgaatac--ttgccatcttaaatggatagtttattcctttcagtgtttagtttatatacttctggttcagactagttcaaagtttagttatccaatccat

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G31350.2 (Arabidopsis thaliana), 5'ss of exon 4
GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatatctggat-----ttcgtacttttgaaacatgtgatcatttca--aaatcaactgatg-aaaacagtacatttctt
|| || ||||||||||||||||| |  ||||| ||||| ||||| ||||||||||| |||||||| ||   ||| || || |||||||| || ||   ||||  | | | ||    |     | |     |  | || ||     ||| | | ||  |   | |   |   ||    ||||   |   |  |||  |||         
GACCGGATTCCTGGAATTGATATGGCCTTGAAGGATGGTGACAAATGGATGTTTGCTGGCCATGAAGTCCATGTTATGGATACTCCTGGCCACACAAAAGgttgtttataattctcatattaacttttggagctttgaatgcatgttcttgcattccagttaagcctttgctttgctaaatattccactttaaagtagtt--------

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|77584541|gb|DV221342.1|DV221342
EST:     GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAG                         GCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
genomic: GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
EST: gi|110404767|gb|EC970289.1|EC970289
EST:     GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAG                         GCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
genomic: GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
EST: gi|110708395|gb|EE085884.1|EE085884
EST:     CCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAG                         GCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
genomic: CCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
EST: gi|110718180|gb|EE094717.1|EE094717
EST:     GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAA                         GCCACATTAGCTTCTACTTTCCGGGATCANGGGCAATTTTTACAGGGGACA
genomic: GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
EST: gi|110715392|gb|EE093393.1|EE093393
EST:     GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAG                         GCCACATTAGCTTCTACTTTCCGGGATCANGGGCAATTTTTACAAGGGACA
genomic: GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
EST: gi|34549778|gb|CF518010.1|CF518010
EST:     GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAG                         GCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
genomic: GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
EST: gi|110688962|gb|EE068114.1|EE068114
EST:     GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAG                         GCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA
genomic: GTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttc ... ttgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGAATTCCTGGAATTGATATAGTTTTGAAAGATGGAGACAAGTGGATGTTTGCAGGCCATGAGGTGGTTGTAATTGAAACTCCTGGTCATACCCGAGgtcatatttcatcactaatcatattagaaaatatctggatttcgtacttttgaaacatgtgatcatttcaaaatcaactgatgaaaacagtacatttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaca