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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgattgtgtgcaccatgattttatgtaatgattaattttatattgtcctcttcttccatcatcactagcttttctcatggaagtatatgttggaaaaatggtgttccccag

Basic information

species Vitis vinifera
transcript Vv08s0040g00430.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 9
ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcg-attgtgtgcaccatgattttatg--taatg-attaattttat-attgtcctcttcttccatcatcactagcttttctcatggaagtatatgttggaaaaatggtgttccccag
||| || ||||| |||||||||||||| ||||||||| |||||||||| ||||| || ||||| |||||||| ||||| |||||  ||||||||     |||| ||  | || ||   ||||  |  || | |||||| |  ||       |||| | ||  |   |    | | |   |||| |  || ||||  || |  |  |  ||||
ATACAAGAATGACCCTGAAATTTTGGCAATGACAAATTTGATAGCAGCCTATCAGCGTAATGAAATATTGGAATTTGAGAAAATCTTGAAGgtacttttattgagtctagcaagagaatatgtctgctgcactaatttgaccataaagtatttctcctatttttcatccaatatttgtcggaatttgattttgggtaatt--tactttccag

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 9
ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcg-attgtgtgcaccatgattttatgtaatgattaattttat-attgtcctcttcttccatcatcactagcttttctcatggaagtatatgttggaaaaatggtgttccccag
||| || ||||| |||||||||||||| ||||||||  |||||||||| ||||| || ||||| |||||||| ||||| |||||  ||||||||     |||| ||  | || ||   |||||    | ||| || |  ||       ||||   ||  |   |    | | |  ||||| |  || || |  || |  |  |  ||||
ATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAGgtacttttattgagtctagcacgagaatatgtctgcactaacttgaccataaaatatttctcttatttttcatccaatatttgttggaatttgatatttggtaagt--tactttccag

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 9
ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcg-attgtgtgcaccatgattttatgtaatgattaattttatattgtcctcttcttccatcatcactagct--tttctcatggaagtatatgttggaaaaatggtgttccccag
||| || ||||| |||||||||||||  ||||| ||  | ||||| || |||||||| ||||| |||||||| ||||| |||||||||||||||     ||||  |   ||||||  |||||  || | || ||| |  ||    | ||  |||    |   || ||  |   | ||  || |  || ||| | ||   ||  |  ||||
ATACAAGAATGACCCTGAAATTTTGGTGATGACTAACTTAATAGCGGCTTATCAACGTAATGAAATATTGGAATTTGAGAAAATTCTGAAGgtacttttattgaatctgccatgagattatgctat-actagtttgactttaaagtatttatcctcgttttgtatctaatactttatttaaatggatattgcataat--gtactttccag

upper sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 5'ss of exon 9
ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgattgtgtgcaccatgattttatgtaatgattaattttatattgtcctcttcttccatcatcactagcttttctcatggaagtatatgttggaaaaatggtgttccccag
 || ||||| || ||||| |||||||| ||||||||| |||| |||||||||||||| ||||||||  | |||||||| | ||| || |||||||    |   ||       | || | | |    | | ||| ||||| |    |  |   |||    | | | ||||   ||| |                              
GTACAAAAACGACCCTGAGATTTTGGCAATGACAAATTTGATCGCAGCATATCAACGAAATGAGATCATAGAGTTTGAGAGAATACTAAAGgtaaaaagtgaagtattattgggttgtttttt-caactcattatatat-gaaaacgacactcatgg--aatggtttttggaatgtag-----------------------------

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|110363999|gb|EC927636.1|EC927636
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAATTTCTGAAG                         AGTAATAGAAGAACAATCATGGATGATCTTTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
EST: gi|33405471|gb|CF211098.1|CF211098
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG                         AGTAATAGAAGAACAATCATGGATGATCTCTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
EST: gi|33405408|gb|CF211035.1|CF211035
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG                         AGTAATAGAAGAACAATCATGGATGATCTCTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
EST: gi|22015265|gb|BQ800299.1|BQ800299
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG                         AGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
EST: gi|110703379|gb|EE080173.1|EE080173
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG                         AGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
EST: gi|33402297|gb|CF207924.1|CF207924
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG                         AGTAATAGAAGAACAATCATGGATGATCTCTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG
EST: gi|33402377|gb|CF208004.1|CF208004
EST:     TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAG                         AGTAATAGAAGAACAATCATGGATGATCTCTTCATCAGAAATTACATCGAG
genomic: TAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgatt ... tgttccccagAGTAATAGAAGAACAATTATGGATGATCTCTTCATCAGAAATTACATCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATAAAAATGATCCTGAAATTTTGGCCATGACAAATCTGATAGCAGCATATCAACGCAATGAGATATTGGAGTTTGAAAAAATTCTGAAGgtaagcgattgtgtgcaccatgattttatgtaatgattaattttatattgtcctcttcttccatcatcactagcttttctcatggaagtatatgttggaaaaatggtgttccccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG