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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG

Basic information

species Vitis vinifera
transcript Vv12s0134g00150.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G11710.1 (Glycine max), 3'ss of exon 5
gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG
    | |||| |  |||||||||  || || | | ||           || |  |  || |  ||| ||     |   ||  |||  |  |||| | | ||||||||| ||||||||||| |||||||| ||  |||| || ||  |||| |||||||||||||||||||| ||||| |||||  | |||||||||||| ||
---gtatttttcttaagatccttttttgttattgatta----------tgtaagagcttactgtatttttaactaaaatcc-actgaattatttgtct-tagGTTCTCATATATTGCTATTTGTTGTCTATCAATATTACATTGCTTGGATAAAATCAATGTGGAGAAGGCAGTGAAGTACATTATAAGTTGCAAAAATATG

upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G28630.1 (Glycine max), 3'ss of exon 4
gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG----------------------------------------------------------------------------
    | |||| |  ||||| |||  ||||| | | |            || |  |  || |  ||| ||     |   ||  |||  |  |||| |   ||||||||| ||||||||||| |||||||| ||  |||| ||  |  |||| |||||||||||||||||||||||||| |||||  |   ||         |                                                                             
---gtatttttcttaagattcttttttattattgatca----------tgtaagagcttactgtatttttaactaaaatcc-actgaattatttgtcc-taggttctcatatattgctatttgttgtctatcaatattacatcgcttggataaaatcaatgtggagaaggctgtgaagTACATTATTTTTTTTTTCTTCGTACCCCATTGCCCAGAGGCTCTTCGCTATGCGAAGGTATGGGGGAGGGATGTTGCACGCAGCCTTACCCTTGCATATG

upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 5
gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG
|| || ||     | |  |  | ||          || ||   |    ||  |    ||||  ||||||     | ||| | ||   |   | ||| || ||||| || || || ||||| || ||||||||  ||||| ||||||| ||||||||||||||||||||||| || || ||||| ||||| |||||||| |||
gtgtttttccttgccatgtattacaaagac----atttatatatttcctgttggtgatttcactatgtt----gaatct-taacagcaagctgtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG

upper sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G12070.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG
|||||||||      || |  ||  |||||| |  ||               || ||||||  ||||||       |||   |   |     |||  |||||||| ||||| || |||||||| || |||||  ||||  ||||||| || |||||||||||| ||||||||||  | ||||| ||||| |||||||| |||
gtattctttcttcatagctttttgtttattccgattt---------------gtgagtttcattatgttt-----atctgcaagcttg----tttaatgtagGTTTTCTTACATAGCTATATGCTGCCTCTCAATATTAAAATGTCTTGATAAAATCAATGTGAAGAAGGCTGTTGATTACATTGTGAGCTGCAAAAACCTG

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|349826932|gb|FQ419023.1|FQ419023
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|161712241|gb|FC061615.1|FC061615
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTG
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTG
EST: gi|351047683|gb|FQ455080.1|FQ455080
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|351032822|gb|FQ461711.1|FQ461711
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|349810206|gb|FQ401652.1|FQ401652
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|161721200|gb|FC071051.1|FC071051
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|349817650|gb|FQ407639.1|FQ407639
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|349809279|gb|FQ399053.1|FQ399053
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|351015754|gb|FQ431709.1|FQ431709
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|351045119|gb|FQ449373.1|FQ449373
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|349815323|gb|FQ400478.1|FQ400478
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|349807995|gb|FQ402386.1|FQ402386
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
EST: gi|351045348|gb|FQ451796.1|FQ451796
EST:     AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACG                         GTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA
genomic: AATGTAGATGGGTCCTTTTCAGGTGACATGTGGGGTGAAATTGATACACGgtattctttt ... ttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG
                              ctctgac  putative branch site (score: 3)
                                            tttttttgt  putative PPT
                                     tatagaatttttttgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA