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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaacccttgatttttatttatgttacatgttgggatttgtttctgttgctcattttgtaatttgcag

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 4
TCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaacccttgatttttatttatgttacat--gttgggatttgt-ttctgttgctcattttgtaatttgcag
||||||||||||||||| || |||||||||||||||||||||||  | || ||||| ||||| || ||||||||||||||||     | ||| |     |||||||||| ||   ||    ||||| ||||  |  | |||   |  |||||||
TCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttgctctttag----atttatgttaaattgatttcattttgtattctaattttaattcaatgctttgcag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 4
TCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaacccttgatttttatttatgttacatgttgggatttgtttctgttgctcattttgtaatttgcag
||||||||||||||||| || |||||||||||||||||||||||  | || ||||| ||||| || ||||||||||||||||     |  || |  ||||| |    |  || |     | ||||    || || |||   |  |||||||
TCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaatt-ctaattcaatgctttgcag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 4
TCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaacccttgat--ttttatttatgtta-catgttgggatttgttt-ctgttgctcattttgtaatttgcag--------
||||| ||||||||  | |||||||||||||| ||||| |||||  |||||||| ||||||| ||||||||||||||||||| |  |   || ||  |||  ||  | |   | | ||    || |  | || ||| | |  || ||||   |          
TCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCTgtaaggaacaattttcatagtttccttcctctcctcttcttatcgttcgaatgcttttgtttaggttataatcgtcgagtttacag

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 5'ss of exon 4
TCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaa---------gaacccttgatttttatttatgttacatgttgggat-ttgtttctgttgctcattttgtaatttgcag
||||| ||||||||  | |||||||||||||| |||| ||||    |||||||| || |||| |||||||||||| ||||||||         ||  | |     |||  |||    |  | ||    | || | |  | |  | || ||| | ||  |||
TCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATATgtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacag

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|161716028|gb|FC065534.1|FC065534
EST:     GATCGCAGATCTGCTGCCTTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|349811318|gb|FQ407544.1|FQ407544
EST:     GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|161705670|gb|FC055790.1|FC055790
EST:     TCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: TCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|161721264|gb|FC069684.1|FC069684
EST:     GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|110694202|gb|EE071104.1|EE071104
EST:     GATCGCAGATCTGCTGCCTTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|110696392|gb|EE072470.1|EE072470
EST:     CTGCCTTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: CTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|351031018|gb|FQ439054.1|FQ439054
EST:     GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|161707025|gb|FC055133.1|FC055133
EST:     TCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: TCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|27755123|gb|CB035878.1|CB035878
EST:     GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|77582239|gb|DV220083.1|DV220083
EST:     GATCGCAGATCTGCTGCCTTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
EST: gi|110357183|gb|EC920553.1|EC920553
EST:     GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCT                         GTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA
genomic: GATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaa ... taatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTgtaagaagaacccttgatttttatttatgttacatgttgggatttgtttctgttgctcattttgtaatttgcag

- - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - TGCTGC