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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtcacataaagtttcctaatttagaaagctatgcttcaagcattatccagaatgtaatattggtccttctctgcattcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATAGAGCACAGTGTTGTCGGTATCAGGTCCCGTGTAAACTCCAATGTTCACT

Basic information

species Vitis vinifera
transcript Vv05s0020g02880.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 11
gttggtcacataaagtt-tcctaatttagaaagctatgcttcaagcattatc------cagaatgtaatattggtccttctctgcattct---tctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATAGAGCACAGTGTTGTCGGTATCAGGTCCCGTGTAAACTCCAATGTTCACT
 ||  |    ||      ||| |   |||| | | |    |     | | ||      || | |  || |||| |  || |||   || |   ||||||||||||||||||||| |||||||||||||||||||| || |||| ||||||||||||||||||||| || ||||| ||| |  ||||||| ||| ||||||
tttcctgctgtatccccatcccacactagacaaccagctcttttctactttcaaatctcaaactacaacattgttatttgtctcttttttttgtctgcagATTGTTGATTCAATTATATCACATGGAAGCTTCTTGAATAATTCCTTCATAGAGCACAGTGTTGTTGGAATCAGATCCAGAATAAACTCAAATATTCACT

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 11
------------------------------------------------gttggtcacat-aaagtttcctaatttagaaagctatg-----------cttcaagcatta---tccagaatgtaatattggtccttctctgcattcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATAGAGCACAGTGTTGTCGGTATCAGGTCCCGTGTAAACTCCAATGTTCACT
                                                  | |    |  ||||  |  |   || |  |  | ||            ||| |   | |     || | |  || |||| | ||| ||  | |  || ||||||||||||||||||||||||| |||||||||||||| || |||| |||||||||||| || ||||| || ||||| ||| |  ||||||| |||||||| |
gtcagttcttcaaacttgctcctgtgagaaattttttaagtatttcacactagaagtaccaaagccttattgctttgggaagtgtgaacttacctcttttctactttcaaatctcaaactacaacattgttacttgtc--cttctttatgcagATTGTTGATTCAATCATATCTCATGGAAGCTTCTTGAATAATTCCTTCATAGAGCATAGCGTTGTTGGAATCAGATCCAGAATAAACTCAAATGTTCATT

upper sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 11
gttggtca-------cataaagtttcctaatttagaaagctatgcttcaagcattatccagaatgt--aatattggtccttctctgcatt-cttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATAGAGCACAGTGTTGTCGGTATCAGGTCCCGTGTAAACTCCAATGTTCACT
||  || |       ||| |  ||||||  |||||     | |  ||      |  ||||   | |  |  |||    |||   |  ||| | | || || |  | ||||||||||| || |||||||||||||||| ||| ||||| || ||||| ||  |||| || || || ||  | |||  |   |||||||| |
gtaagtaaaaccagccatgatatttcct--tttagttctatgtattttggtgttggtccattttcttcaggattaactcttaagtttattacatgtgaagCTCATCGATTCAATCATTTCTCATGGAAGCTTCTTAACCAACTGCTTGATTGAGCATAGCATTGTGGGAATTAGATCAAGAGTAGGCAGTAATGTTCAGT

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|110379176|gb|EC944355.1|EC944355
EST:     TGTACACATCAAGAAGAAATT-ACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGAAAACCTTCTTAA-CAATTGC
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGC-TTCTTAAACAATTGC
EST: gi|351029658|gb|FQ427498.1|FQ427498
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTTATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351040871|gb|FQ438415.1|FQ438415
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTTATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351019209|gb|FQ429369.1|FQ429369
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTTATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351025236|gb|FQ433653.1|FQ433653
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTTATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351013646|gb|FQ429787.1|FQ429787
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTTATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351015482|gb|FQ447311.1|FQ447311
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351034082|gb|FQ448000.1|FQ448000
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTTATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
EST: gi|351013342|gb|FQ425047.1|FQ425047
EST:     TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAG                         ATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA
genomic: TGTACACATCAAGAAGAAATTTACCACCTTCAAAGATCGATGATAGCAAGgttggtcaca ... tcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttcaagcattatccagaatgtaatattggtccttctctgcattcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATAGAGCACAGTGTTGTCGGTATCAGGTCCCGTGTAAACTCCAATGTTCACT
                                tccttctctgcattct  CT-rich tract
                   aatgtaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtcacataaagtttcctaatttagaaagctatgcttcaagcattatccagaatgtaatattggtccttctctgcattcttctgcagATTGTTGATTCAATCATATCACATGGAAGCTTCTTAAACAATTGCTTCATAGAGCACAGTGTTGTCGGTATCAGGTCCCGTGTAAACTCCAATGTTCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA