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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaactctaatattagattgttactatttatgtgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcag

Basic information

species Vitis vinifera
transcript Vv03s0038g01780.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 5
TGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaa------aaactctaat---attagattgtta--------------ctatttatgtgaaacgtgaagctata---ttcagaa--ctttttttttttggataagtgaagct-atattcagaactt--gactgtgggtctgaaattttcag-------------
|| ||| ||||||   || ||||||||| | |||||||| |||||||| || ||| | |||||||| |||||||||||||||||||| |       | || |  ||   | | ||||| ||              | | || |       || |  || ||   ||| |||  |   |||    || || | ||  | | | || ||| | ||  || || |  | ||| ||     |             
TGCGGAGCAATTGGTGGACATTGGCTGCCAATGGGTTATTCTTGGGCATTCAGAGCGTAGACATGTCATTGGTGAAGATGATCAGgtaagcgctatatacacagatgctactggattggtagttctctcacttgtccacttgtccatgctgttagcctgtaacattctgaaggcacctttgagatgcatgattgctgttgacatgcagtagttctgattgggattgtgacataccatgtttataaatgcag

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 5
TGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaactctaatattagattgttactatttatgtgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcag
||  |||||| ||   || || |||||  | |||||||| ||||| ||||||||| | |||||| ||||||||||| ||||| ||||||  |  | | ||       || ||||  ||   |||||| || ||    | ||| |  || |  ||     ||||   ||| | |  ||| |    |                      
TGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAGgtgatta--ttttatgcgcatgtgctactggtt---tgaaacttggag----aatcacagtttctgattacaatataac--aagttgt--tcaaatgcag----------------------

upper sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G34300.1 (Glycine max), 5'ss of exon 5
TGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaa--aaactctaatattagattgttactatttatg-tgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcag
 | ||||||| | |||||| |||| ||||| |||||| | ||||| || |||||| | |||||||||||||| ||| ||||| |||| ||  ||| ||  | || |  |    | ||  | || ||    |  |    ||||    ||  | |||      ||| |   ||   ||||| |  |  | |||       ||  |  | |||
CGCGGAACAACTAAAAGATCTTGGATGCAAGTGGGTTGTTCTTGGACATTCTGAGCGAAGACATGTTATTGGAGAAAATGATGAGgtaaagcaaattcagaaatcatttctacagtagctttgctgctttgctagagaatatgattaatatatttgcaagagatgatgcaaa--atatttaagatcttacttgaatattgtcaactccag

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|110730538|gb|EE107734.1|EE107734
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|34545318|gb|CF513550.1|CF513550
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110713056|gb|EE088645.1|EE088645
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110692798|gb|EE068468.1|EE068468
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|27580841|gb|CB003536.1|CB003536
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATG
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATG
EST: gi|352798567|gb|FQ480592.1|FQ480592
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|161721774|gb|FC070490.1|FC070490
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|27580521|gb|CB003216.1|CB003216
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110713655|gb|EE089776.1|EE089776
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATANGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|351015203|gb|FQ445487.1|FQ445487
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|351055931|gb|FQ453392.1|FQ453392
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|161719285|gb|FC068261.1|FC068261
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|351042327|gb|FQ442794.1|FQ442794
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110687322|gb|EE064629.1|EE064629
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|33406430|gb|CF212057.1|CF212057
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|161715107|gb|FC064265.1|FC064265
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|351038588|gb|FQ464454.1|FQ464454
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|30297140|gb|CB973934.1|CB973934
EST:     TTATCCTTGGGCACTCTGAGAGGAGACACGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|30321727|gb|CD004989.1|CD004989
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110684631|gb|EE062130.1|EE062130
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|351044839|gb|FQ449093.1|FQ449093
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGANAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|27578848|gb|CB001543.1|CB001543
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110705429|gb|EE082267.1|EE082267
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|294966365|gb|GW837616.1|GW837616
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110720871|gb|EE097170.1|EE097170
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|352790810|gb|FQ478533.1|FQ478533
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|56408461|gb|CX016713.1|CX016713
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|351036824|gb|FQ459346.1|FQ459346
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
EST: gi|110721976|gb|EE097800.1|EE097800
EST:     TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAG                         TTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA
genomic: TTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaact ... aaattttcagTTCATAGGAAAGAAAGCTGCTTATGCCTTGAGCCAGGGTCTTAAAGTAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGGAACAATTGAAAGATATTGGCTGCAACTGGGTTATCCTTGGGCACTCTGAGAGGAGACATGTTATTGGTGAAGATGATCAGgtgaaaaactctaatattagattgttactatttatgtgaaacgtgaagctatattcagaactttttttttttggataagtgaagctatattcagaacttgactgtgggtctgaaattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG