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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag

Basic information

species Vitis vinifera
transcript Vv05s0020g03880.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os07g07974.1 (Oryza sativa), 5'ss of exon 6
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTG--GGgttaggacataattcttgccttgtgttta-tacagaaaatctgaactgctagttaccctgttaagtgaggttttctc---ttgcag
    | ||||||| | |||||||||||||| ||||   |||| ||||| ||||||||||| ||||||||  | |  |||||| ||   | |||  ||   ||| ||||   |  ||  ||  | || | || |||    |  |   | | | | |||    ||   |  |   ||       ||||||
---GATTGTTCTTTCCACTCGCAAGCAGATAGAATTCAGGAACCCACTGGCATTTGCTCCAAAAGTGATCCGCATGTCTGATGCTGGTCAGGATATTACTGGGgtaggcgctttttgctggatagtctgtactacttctagccctcatttccatttatgtggtgctgaaatacttcaataaattgcag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g43730.1 (Oryza sativa), 5'ss of exon 9
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag
 || || ||| |  | |||||||| | ||| |||||||| ||||||||||| |||||||| ||||| ||| | |  | ||   ||   | |||  ||||||| ||  || | | |||    | |  || |        ||   | ||||  | ||  | ||      ||  |          
GGAAACAGTTTTATCTACTCGCAATCGGATTGAATCTCGTAATCCACTAGCTTTTGCTCCAAAAGTAATTCGCACTTGTGGGCCTGGTCTGGAGTTTGGGgtaagagcacattccttttgcttttcttttctg-----tcattattgctcataacgttctttttcatggcatag--------

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G701689_T01 (Zea mays), 5'ss of exon 6
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttag-gacataa--ttcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag
 || ||||||||  | || ||  | ||||| |||||||| |||||| ||||||||||||| ||||| |||   |  |||||  ||   | |||| |  |||| || ||||  |  || |||  |     |  | |    |||||   ||| |  | |     | |  |    | || |       
GGAAACTGTTCTATCTACGCGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTAATTCATACATCTGAGCCTGGTCTGGAACTAAGGgtaagagacactaacttattgtatctgagtacttcccttaatcttgtctgttgctaatatcatcatcttcaatattgtag-----

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G322090_T01 (Zea mays), 5'ss of exon 7
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgtttatacagaaaatctgaact-gctagttaccctgttaagtgaggttttctcttgcag
 || || |||||  | || ||  | ||||| |||||||| |||||| ||||||||||||| ||||| |||   |  |||||  ||  |   | | || ||| || || | | |   |   ||||  ||    |     | | | || |   ||| |     | | ||   ||   |  || ||
GGAAACAGTTCTGTCTACACGGCAACAGATTGAATCTCGCAATCCATTAGCATTTGCTCCTAAAGTCATTCATACATCTGAGCCTG-GTATGGACTTAGGGgtaagagacactaact-tattgtacttgagtatttcctttaatcttgtctgttgctaatatcattgtc-ttcaatactgtag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA11G00920.1 (Glycine max), 5'ss of exon 8
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccc-tgttaagtgaggttttctcttgcag
||| |||||||||  ||||||||||||||| |||||||| || || || ||||||||||| ||||| || || |  ||||||||| | || ||| |||||||||| | ||||      | | || |||   |  |  |  ||||       |||    | |||| |    | || |  || ||
AGACACTGTTCTTCAAACTCGCAAGCAGATTGAATCTCGTAACCCTCTTGCATTTGCTCCTAAAGTCATCAGAAATTCTGATTCTGTACCTGAAATTGGGgttagaaaataaactcgacttagtttttcccctaagcaattgaaacatcttttataggtattaattattatctttt--tgtag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA01G44670.2 (Glycine max), 5'ss of exon 6
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgttt-atacagaaaatctgaactgctagttaccc-tgttaagtgaggttttctcttgcag
||| |||||||||  ||||||||||||||| |||||||| || || || ||||||||||| ||||| || || |  ||||||||| | || ||| |||||||||| | ||||   |  | | || ||| |   |   |||   |||  |   |||    | |||| |    | || |  |||||
AGACACTGTTCTTCAAACTCGCAAGCAGATTGAATCTCGTAACCCTCTTGCATTTGCTCCTAAAGTCATCAGAAATTCTGATTCTGTACCTGAAATTGGGgttagaaaataaacttgacttagtttttcacgtaagcaattgaaaccaccttttatgggtattaattattatctttt--tgcag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G28740.2 (Glycine max), 5'ss of exon 4
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattctt--gccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag
 || |||||||||  ||||||| ||||||| || ||||| |||||||| ||||||||||| ||||| ||  | || ||||||||| |  | ||| ||||||| || | || | | ||   | || | |||        ||| | |||      ||  | | |         |||| ||||||||
TGAGACTGTTCTTCAAACTCGCCAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGGgtcagcaaattaatatttaactttatttttcactttctaatttaaaccatgttttttcatatattaattctttttttcttgcag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G39080.1 (Glycine max), 5'ss of exon 12
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattctt--gccttgtgtttatacaga--aaatctgaactgctagttaccc---tgttaagtgaggttttctcttgcag
 || |||||||||  ||||||| ||||||| || ||||| |||||||| ||||||||||| ||||| ||  | || ||||||||| |  | ||| ||||||| || | || | | ||   | || | ||   ||     || | | |||   |  ||   |   | |||| |    ||||  |||||||
TGAGACTGTTCTTCAAACTCGCCAGCAGATTGAGTCTCGTAATCCACTTGCATTTGCTCCTAAAGTCATACGAAGTTCTGATTCTGTATCTGAAATTGGGgtcagcaaattaatatttaactttattttctcactttctaattttaaaccatttttttttcatatattaattat--tttttccttgcag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 5'ss of exon 5
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtg-----tttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag
|||   ||| || || |||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||||||| |||||| ||  | |  |||   |||||  |    |  | |  | | | ||     | |  |      ||||    |||| |      |  ||| |   ||  |  |   |||
AGACGTTGTCCTGGCGACTCGCAAACAGATTGAATCTCGGAATCCACTTGCATTTGCTCCTAAAGTCATTAGGAACTCTGACTCAGTTCAAGAAACCGGGgtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataa-tattgtaatgacacacag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 5'ss of exon 6
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttag-gacataattcttgccttgtgtttata-----cagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag
||||  ||| || || |||||||| ||||| ||||| || |||||||| ||||||||||| ||||| || || | ||| |||||  |    |||||||| || || |   | | | || |||| |  ||||      ||  | || |       |    |  || | || |   |  ||   |  |||
AGATGTTGTCCTGGCTACTCGCAAACAGATTGAATCCCGCAATCCACTTGCATTTGCTCCTAAAGTCATCAGAAACTCAGATTCCATCATTGAAGTTGGTgtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacag

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: EFJ04883 (Selaginella moellendorffii), 5'ss of exon 1
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag
    || ||  | | ||| ||  |||| |||||| |||| |||||| ||||||||||||||||| |  |   ||  ||||||      |||   |  |||||| | |  |  || | ||| |      || |    | |   |                                       
----ACAGTCATGGGAACCCGTCAGCAAATCGAAACTCGTAATCCATTAGCATTTGCTCCCAAAATTGTACAGACATCTGATAACACACCGACGGAAGGGGTTGgtatctggttttcgccctcgcgacatgccatgactaacag--------------------------------------

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|110702530|gb|EE081350.1|EE081350
EST:     CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGG                         GATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC
genomic: CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacat ... tctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC
EST: gi|351044072|gb|FQ452745.1|FQ452745
EST:     CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGG                         GATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAA-GAGGATGCAAC
genomic: CATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacat ... tctcttgcagGATGAACCTAGCAAAACTCCAGCTTCAGCACGACACAAAAGAGGATGCAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATACTGTTCTTGCAACTCGCAAGCAGATCGAATCTCGGAATCCACTAGCATTTGCTCCCAAAGTGATTAGGAGCTCTGATTCTTTGCCGGAAGTTGGGgttaggacataattcttgccttgtgtttatacagaaaatctgaactgctagttaccctgttaagtgaggttttctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT