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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataatttaagcaaaaagaattatcattgatgaaacctggtctt...

Basic information

species Vitis vinifera
transcript Vv02s0025g01410.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: LOC_Os01g46750.1 (Oryza sativa), 5'ss of exon 18
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataatttaagcaaaaagaa--ttatcattgatgaaacctggtctt-------
 || || || || ||||| || ||||||||||| ||||| |||||  |||| |||||||||||||| |||||| | || || ||||| || || || ||||||      || || |  ||  || | |||  ||    | |        ||||    ||| || | ||    ||||  || |||||      || ||||| |       
AAAGGCTGTACATCTTGAACCAGTGCCATTTGACATGGACCGTGATTTGATTACTCCAACATATAAAAAGAAGCGCCCTCAATTGCTCAAGTACTACCAGgta---ttgctcattcaaattctcgt-catactgatggcatat--gttgtttac---atacttcacgcgtgtagaacgttctcattttgcttacttggtcctttgaatc

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataa-tttaagcaaaaagaattatcattgatgaaacctggtctt------
 |||||||||||||||||| |  | |||||||| |||||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||| |||||||||      |   |  ||| |||| |      ||     |   | | | |  || |||||  | |        | ||   | ||  ||| ||  |  | |       
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgta------caagttgtcaaattc-tctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA11G02030.1 (Glycine max), 5'ss of exon 17
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgcta-acaatttatggaataa--tttaagcaaaaagaattatcattgatgaaacctggtctt-----
 || ||||||||| |||||||  | | |||||| |||||||| ||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||||      |   |  ||| ||||   || ||| | |     ||  | | |  || |||||    ||||     || ||   | ||  ||| ||  |  | ||     
AAAGGCAGTTCACATTGACCCAATTCAATTTGACATGGAACGCGACCTTATCACTCCAACATATAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgta------caagttgtcaaattct--caggatttcatttcacttcatattgaatagaataggtcttaaagtggaataacctttataaatggaatgttattttttccc

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA05G36910.1 (Glycine max), 5'ss of exon 18
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgta--gctcctctgatcctc-----atattcatgcatgatgtgaacctgcta-acaat--ttatggaataatttaagcaaaaagaattatcattgatgaaacctggtctt
 ||||| ||||| |||||||| || |||||||| ||||||||||  || || |||||||||| |||||||||||| ||| | ||||| ||||| |||||||||    || ||  |  |||      || |  ||| | ||  |||     |  |   |  || |    |   ||||   ||||    |||||   |  ||          
TAAAGCTGTTCATCTTGACCCAGTTCCATTTGACATGGAACGTGGTCTTATGACTCCAACATTTAAGAAGAAGAGACCCGAATTGCTTAAATACTATCAGgtacaaatcgtcaaaaactctggatttaattttgcttcataagaattgaatggatggtggttttcttttcccttaacttaaaatgcctatcaacaaataa----------

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 5'ss of exon 18
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataatttaagcaaaaagaattatcattgatgaaacctggtctt
 ||||  ||||| || || || ||| | || || |||||||| |||||  | |||||||| || || ||||||||||| || ||||| ||||| |||||||||  |    | | | |    || | ||  ||| | |  ||  ||| | |||  |   |||  |        |    | | ||| |  |           
AAAAGATGTTCATCTGGAACCAGTGGCGTTCGACATGGAACGAGACCTTCTTACTCCAACCTACAAAAAGAAGAGGCCTCAATTGCTCAAATACTATCAGgtaattt---taaacat----tttaggc--gatattatgcttataatattttcggttttaaactctctttctattggtgttatttaacag----------

upper sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: PP1S108_163V6.1 (Physcomitrella patens), 5'ss of exon 18
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataatttaagcaaaaagaattatcattgatgaaacctggtctt-
||||| ||| |   | || |||   |||||||||||||| || ||||||||||||||||| || |||   ||  | || ||  |  ||||| | || ||||||       ||   |||| | | |  |   |  ||    |   ||| | ||||   |    |||   || || ||||       ||       | | |  
CAAAGGAGTGCTGTTAGATCCTCAACCATTTGATATGGAGCGCGACCTGATCACTCCAACTTACAAGCTCAAACGACCGCAACTATTAAAACACTACCAGgtactagagttggatctcacaattaatctatacatgttggtaagaaccacttataacagccgttata-aagaacaatttcagaacattcggtgcgctgtgt

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|30125801|gb|CB911140.1|CB911140
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACCACAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
EST: gi|110375957|gb|EC940989.1|EC940989
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
EST: gi|27580341|gb|CB003036.1|CB003036
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
EST: gi|352781554|gb|FQ468398.1|FQ468398
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
EST: gi|32245315|gb|CD711134.1|CD711134
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
EST: gi|27755362|gb|CB036117.1|CB036117
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
EST: gi|110407574|gb|EC973176.1|EC973176
EST:     TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAG                         AATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA
genomic: TCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctc ... tgtgtcacagAATGTTATTGACAAAATGTACAAAAGCATAAACAAGCCCAGTGCCTGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataatttaagcaaaaagaattatcattgatgaaacctggtctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa