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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgcaaactcattatttagataaaaaattttgttgtttggaaatggaaatcaacaaaaatcaggggaataaatcggcagaggtgatggaaagtca...

Basic information

species Vitis vinifera
transcript Vv13s0019g04410.t01
intron # 7
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 7
lower sequence: 13113.m00157 (Oryza sativa), 5'ss of exon 8
ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgcaaactcattatttagataaaaaattttgtt-gtttggaaatggaaatca-acaaaaatcaggggaataaatc-ggcagaggtgatggaaagtca---------
|| |||||||| |||||||||||||||||||||||    || || ||| | |||| ||| ||||||   ||||||| | |||||||||||||  | |   |          | |||| |   ||   || | |||| ||| |     |        |   | || |  ||| |  |    |||      | |          
ACTAGTTATTCATACCTTGATGTTGTTGGAAGGACGACAGTTGTACTAAAGAAGAGAAACGTAGTTGGAGAGCACAATGTTCCTTTCCAGgtactctctgacagataggccttgatacatttttgaatttgattggtaattgtctgaatgttgctgttgtgagactctatctgataagcatgacatctcggctcaactgcag

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G32070.1 (Glycine max), 5'ss of exon 7
ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgcaaactcattat--ttagataaa--aaattttgttgtttggaaatggaaatcaacaaaaatcaggggaataaatcggcagaggtgatggaaagtca
| ||  ||||| |||||||||||||| || || |||||||| ||||||||||| | ||||| |||||||||||| | || ||||||||||||  ||   || | || | |    | |||||  ||| ||| |    | ||  |||||        |  |||   |    ||     |   |  |  |||| |  
ATCAAGTATTCATACCTTGATGTTGTCGGCAGAACTGTGGTGGTTCTAGAAAAAAGAAATGCAGTTCCTGAGCATAATACTCCTTTCCAGgtatttcctaagcccaatgtgaacaaataaataaaaatttctaaaattgatttggaatgtgg-gcatttcacatgttctaacttctaagagcaa--gaaattt-

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G35450.1 (Glycine max), 5'ss of exon 7
ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgcaaactcattatt------tagataaaaaattttgttgtttggaaatggaaatcaacaaaaatcaggggaataaatcggcagaggtgatggaaagtca
| ||  ||||| || ||||||||||| || || |||||||| ||||||||||| | ||||| |||||||||||| | |  |||||| |||||  ||  ||| | || | |       || ||||| || |||    ||  ||  |||||     | |   |||  ||    ||    ||   |  |  |||| |  
ATCAAGTATTCATATCTTGATGTTGTCGGCAGAACTGTGGTGGTTCTAGAAAAAAGAAATGCAGTTCCTGAGCATAATGCTCCTTTTCAGgtatttaccaagcccaatgtgaaaaaataaataaataaatttaaaatt--gatttggaatgtggccatt-tcacaggttctaacttccaagagcaa--gaaattt-

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|71865487|gb|DT014542.1|DT014542
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTAGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|351015486|gb|FQ447315.1|FQ447315
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|71881801|gb|DT030856.1|DT030856
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTAGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|349824067|gb|FQ417454.1|FQ417454
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|351031867|gb|FQ460124.1|FQ460124
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|352790365|gb|FQ478005.1|FQ478005
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|349812777|gb|FQ410419.1|FQ410419
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|349816667|gb|FQ404914.1|FQ404914
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|51052013|gb|CO819346.1|CO819346
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|351051855|gb|FQ455269.1|FQ455269
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|30132659|gb|CB917998.1|CB917998
EST:     ATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: ATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|351045790|gb|FQ440975.1|FQ440975
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTGTAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|349811345|gb|FQ407571.1|FQ407571
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|351048526|gb|FQ448800.1|FQ448800
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|351053182|gb|FQ455639.1|FQ455639
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|349807244|gb|FQ401236.1|FQ401236
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCTATTTTCATGCTTGCAGAGCCATTCATGTTG
EST: gi|110414535|gb|EC980369.1|EC980369
EST:     TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG                         GTTTACTATAATTTCAACCCT
genomic: TAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgca ... tcttatgcagGTTTACTATAATTTCAACCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAGgtgatttgcaaactcattatttagataaaaaattttgttgtttggaaatggaaatcaacaaaaatcaggggaataaatcggcagaggtgatggaaagtca

- - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaa