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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtctgtatctagctctatattgtactggttcttatggtattctgttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA

Basic information

species Vitis vinifera
transcript Vv05s0049g01840.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 9
ttgtctgtatctagctctatattgtactggttcttatggtattctgttttaag-caccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA
||  |  ||| |     | || | |     ||  ||   ||   ||||| ||  ||  ||| |  |  |||||   |      ||||  ||    ||||||||  ||||||| || |||||||| ||  | || |||||||||||||||||   ||||||||| |||||||| || ||| || |||| || |  || || |
tttaccatattttatattgtaatatttcaattggtaatataaaatgtttcaattcaaattctat-tgtttcaaacttatttgttttacaaaaatctgtcagGTTGAAGCTGTTACAGTCCATGCGACTCAGAAGTACTTTGTGACTGCTTCCAAGGATAATACTTGGTGCTTCTACGATATTCCATCAGGATCTTGCCTCA

upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 11
--ttgtctgtatctagctctatattgtactggttc-ttatggtattctgttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA
  || |    || ||   || |  || ||  ||   || |  |  |||  |||| ||||        | || |||||||||  |   | || | | || |||||||||||||||||| |||||||| || ||||| ||||||||||||||||| || |||    | |||||||||||||| ||||| || ||    ||| |||
gcttctagtgatatatgactttcctgaacctgtcaattgtacttctcttgtttatgcactcct--tctgatgcaagaatgatttgcatttccaatttt-tcagGTGCAAGCTGTCACTGTCCATGCAACCAATAATTACTTTGTGACTGCTTCACTTGATGGCTCTTGGTGCTTTTATGAACTTTCTTCAGGGACGTGTTTGA

upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G26870.1 (Glycine max), 3'ss of exon 11
-ttgtctgtatctagctctatattgtactggttc--ttatggtattctgttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA
 |   ||  || ||   || |   | ||  ||    || |  |  |||  |||| |||| |      | || |||||||||  |   | || | | || |||||||||||||||||| |||||||| || ||||| ||||||||||||||||| || ||     | |||||||||||||| ||||| || ||   ||||||||
ttctactaaatatatggctttcccgaacctgtcaaattttactcgtcttgtttacgcacttct--tctgatgcaagaatgatttgcctttccaatttt-tcagGTGCAAGCTGTCACTGTCCATGCAACCAATAATTACTTTGTGACTGCTTCACTTGACGGCTCTTGGTGCTTTTATGAACTTTCTTCAGGGACATGTCTGA

upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G04510.2 (Arabidopsis thaliana), 3'ss of exon 11
--ttgtctgtatctag-----ctctatattgtactggttcttatggtattctgttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA
    |  |||| ||        |||| |   ||| |  || ||  || ||  ||||||   |  ||     |  || | | |  |   | | ||    | ||  ||||||| |||||| || ||||| || || ||||| ||||||||| | || || || || | |||||||||||| |||||||| || || |||||||| ||  
gtaaggatgtaactgaagaacttctacaggctacagtctcatacagttttacgttttatttatttttggtctgtttaacgtaaaa-gcaatgatgtggtttt--cagGTGCGAGCTGTAACTGTCCACGCAACGAATAAATACTTTGTGTCAGCATCACTTGACAGTACATGGTGCTTCTATGATCTGTCCTCCGGTTTATGCCTTG

upper sequence: Vv05s0049g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G33340.3 (Arabidopsis thaliana), 3'ss of exon 11
--ttgtctgtatctagctctatattgtactggttcttatggtattctgttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA
    |  || || |       | ||  | |   |   ||| | || |  || |   || ||     ||| |  ||       || | ||   || |  |||||||| |||||| || || ||| |||||||||| ||||||||  | || ||||| |||  |||||||||||| || ||||| || ||||| | ||| ||  
gtaaggatgaatttgaggaactcttacagtccgttccatgttcttttaattcatatactttttgtgtaactttagt------taatgat--gctttattcagGTGCGAGCTGTAACTGTGCATCCCACAAATAAATACTTTGTCTCGGCATCTCTTGATGGTACATGGTGCTTCTACGATCTGTCCTCTGGCTCATGCCTTG

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|37184349|gb|CF603703.1|CF603703
EST:     ATAATGAGAACTATAATTGCCGGCACATCTTGAAGGATCATACTGCAGAG                         GTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCT
genomic: ATAATGAGAACTATAATTGCCGGCACATCTTGAAGGATCATACTGCAGAGgtatatcaat ... ctcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA
                                             ctcttgtc  CT-rich tract
                            aatgacatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtctgtatctagctctatattgtactggttcttatggtattctgttttaagcaccttcaacataattcaagaatgacatatttatcaactcttgtcagGTGCAAGCTGTCACGGTCCATGCCACAAATAACTACTTTGTGACTGCTTCTCTGGATAATACATGGTGCTTTTATGATCTTTCATCTGGTTTATGTCTGA

-tgtctgt
- - - - - - - - - - - - - ctggttc
- - - - - - - - - - - - - - - - - - - - - - - - - - -caccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaagaa