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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG

Basic information

species Vitis vinifera
transcript Vv05s0029g01310.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g63090.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------aagtcatagctcttgaattctttctttt--ttacttagaacagtttcctgtttg------caaatttttgcttagtttcatttgtttctctgg---tggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG
                                           |  | |||  | ||   || | |  |     || |  ||  ||  | |  ||||      || |   |||| |    ||| | || |  || |   | ||||| ||| ||||||||||| || || || || ||||||||||| ||||||||||| ||||| || || ||||| || ||||| || || || |||||||||
gtggttttccttcttgatgatctgtttcaatgctctttagccaattttatacgttttctgttatctgctgaaagtattaggagtagactgcattttgtcaagtcagagcattgcatgacatcactggtctaacttggttttgttcatttt-cagGGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G118586_T01 (Zea mays), 3'ss of exon 6
aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctc-tggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG
|   |  |||| |   |   | ||    | |||    |    |||     |  ||||| || |     |  | | ||  |   |  ||  | |  || ||||| ||||| || || || || ||||||||||| || |||||||| ||||| || |||||||| || ||||| ||||||||||||||||||
agagctcagctttaccaagttatcaacataactgcttatcccttcagaaatctaaattgtt-cacgactgaactggtggcaaattatgccttatgtttcagGGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAG

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G28650.1 (Glycine max), 3'ss of exon 6
aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG
                 ||     |  ||||| |||  |  ||||   || | || || |   | |   |   | ||    ||| || | |  || |||||| |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| |||||||| ||||| |||||||||||||||
---------------gtttagcattaatttacatagttcgatttctc-ttagtaacttgtcagtgatcattgat-gtcatcctgttgctcctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAG

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G11740.1 (Glycine max), 3'ss of exon 6
aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG
            || |    |   || | |||||  |    |||  || |  |   ||  || | | |      |||    ||| || |||  || |||||| |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||| || ||||| ||||| |||||||||||||||
-----------gtttagcattgatttatatacttccatt--ttttttggtaacgtgttagtgatcattgg----tgtcatcctgttgcttctgttggcagGGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAG

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G14147.1 (Arabidopsis thaliana), 3'ss of exon 7
aagtcatagctcttga--attctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG
  | | | ||| | ||   ||   | ||| || |   | |  || |      | ||     ||  |   ||  ||| |||||| || ||||    |   ||||| |||||||| |||||||||||||||||||| ||||| || || ||||| ||||| ||||| |||||||| ||  | || |||||||||
--gccttggctttagatggtttactgtttattcccctgcattgtgtgaacgatccattcccttattcccttcaattggtttctttgttggtgttttgaacagGGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAG

upper sequence: Vv05s0029g01310.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G14147.2 (Arabidopsis thaliana), 3'ss of exon 7
aagtcatagctcttga--attctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG----
  | | | ||| | ||   ||   | ||| || |   | |  || |      | ||     ||  |   ||  ||| |||||| || ||||    |   ||||| |||||||| |||||||||||||||||||| ||||| || || ||||| ||||| ||||| |||||||| ||  | || |||||||||    
--gccttggctttagatggtttactgtttattcccctgcattgtgtgaacgatccattcccttattcccttcaattggtttctttgttggtgttttgaacagGGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGGCAA

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|29785136|gb|CB341880.2|CB341880
EST:     TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
EST: gi|71855533|gb|DT004588.1|DT004588
EST:     TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTG
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTG
EST: gi|351046852|gb|FQ454462.1|FQ454462
EST:     TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAGCCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
EST: gi|71857830|gb|DT006885.1|DT006885
EST:     TGTCAATGAGGGCAGAAGCATTTCGAGTATTGAGGAGAAAACCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
EST: gi|110693326|gb|EE069458.1|EE069458
EST:     TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
EST: gi|349826081|gb|FQ415886.1|FQ415886
EST:     TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAGCCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
EST: gi|33405119|gb|CF210746.1|CF210746
EST:     TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAG                         GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA
genomic: TGTCAATGAGGGCAGAAGCATTTCAAGTATTGAGGAGAAAACCAGTGCAGgtatgtatgg ... cactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG
                                           ttcacttt  CT-rich tract
        aaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtcatagctcttgaattctttcttttttacttagaacagtttcctgtttgcaaatttttgcttagtttcatttgtttctctggtggttcactttgcagGGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - gctcttg
- - - - - - - - - - - - - - - - - agaacag
- - - - - - - - - - - - - - - - - - - - - ttcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtt