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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag

Basic information

species Vitis vinifera
transcript Vv03s0038g04470.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g50616.1 (Oryza sativa), 5'ss of exon 4
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag
||||| ||||||  ||||     | | ||||||||| ||  | ||||||||||| ||||||||||||||  |||  ||||| |||||||| ||||| |||||||| | | |   |     |||||    | || || ||| || || |||    || |  | |||  ||||| | |||| | |                     
GGAGTCCGAGAAGTGCTTGCAGATGAGGTTTCCAGCTTGCTCCATTGCTGCAAAAAGGCACATAGATTCGTGCAGTACTATCTTGGATGTGCAAGGAGTGgtatgttattttatagccaatcttg----ctatcgccaaa-at-ttctgggtagattagta-gtt--aacttgttttttatgtgaag-----------------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G171354_T03 (Zea mays), 5'ss of exon 5
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag
|||||| ||||  |||||     | || |||||||| ||  || |||||||||| |||||||| |||||||||||||| ||| ||||||| || ||||||||||| |       ||||  ||||        |    |    | | || |  |||    |  ||| |    |     ||  ||  ||     |||         
GGAGTTTGAGAGGAGCTTCTTGATTAAATTTCCAGCTTGCTCTGTTGCTGCAAAAAGGCACATTGATTCCAGCACAACAATTCTGGATGTCCAGGGCGTGgtatgttactgaggatttaatctt--------tcatgatgcttttctttgtgcaacttgacagttgatgagtgctactttcatacctatgtttcatag------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G174990_T02 (Zea mays), 5'ss of exon 5
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatca-tcaattttccag
 || || |||||  ||||     | || |||||||| || || |||||||| || | ||||||||||||   ||| |||||||||||||| ||||||||||||||||       ||| |  ||  ||     |    | |||||      |      || | ||| | ||||   | ||   ||  || | | ||||        
AGAATTTGAGAAGTGCTTCCAGATGAAATTTCCAGCTTGCACCATTGCTGCTAAAAAGCACATAGATTCGTCCACTACTATTTTGGATGTGCAAGGCGTGgtatgctgcactatattatagctaagtattgttctttacatataaagccacattgctaaga-gttaatactttgttctttacttcttggtaaatcaag-------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G073571_T03 (Zea mays), 5'ss of exon 4
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatct--tttctatttctgatcatcaattttccag
|||||| ||||  |||||     | || |||||||| ||  || |||||||||| |||||||| ||||||||||| || ||| ||||||| || || ||||||||         ||||  ||||  |||  ||       | | ||   ||    ||| |||   | | || ||    |  ||||   | ||              
GGAGTTTGAGAGGAGCTTCTTGATTAAATTTCCAGCTTGCTCTCTTGCTGCAAAAAGGCACATTGATTCCAGCACGACAATTCTGGATGTCCACGGAGTGgtatgtcactgaagatttagtctt--tcatgatgct----tctcttcatgcaacttcacaattggtgagctaattagatacctatgctttatag------------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 4
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgt---atgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag
|||||| ||||||   |||||  | |||||||| || ||  |||||||||| ||||||||||| ||||||||||| || || || |||||||| || |||||   ||| |  || |||||||||  |  || |  || | |     || |          || ||    | |||| | || | |  ||   || ||||         
GGAGTTTGAGAAAGCTTTTGCAATCAAGTTTCCTGCTTGCTCTATTGCTGCCAAGAGGCACATTGATTCCAGCACCACAATCTTAGATGTTCACGGAGTGgtattatgttacctctaatttttttatcttcgcatttactactgtaatctaaagttctataacataca-agacttttgttgtatgattgacattatcag--------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G01220.1 (Glycine max), 5'ss of exon 4
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgta---tgctttctgtaattttt--tcttgg---tcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag
|||||| ||||||   |||||  | |||||||| || ||  |||||||||| ||||||||||| ||||||||||| || || || |||||||| || ||||||   || |  || ||||||||  |||| |   | || | || ||| || | ||       ||  || |    | | || | || | || ||   |||||||         
GGAGTTTGAGAAAGCTTTTGCAATCAAGTTTCCTGCTTGCTCTATTGCTGCCAAGAGGCACATTGATTCCAGCACCACAATCTTAGATGTTCACGGAGTGgtattatgttacctctaatttttcatctttgcgttgactactgtaaactaaagttatataacatacaagta---acatttttgttgtataattgacatcatcag--------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 4
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag
|||||| ||||||   |||    |||||||||| || || || ||||| || || |||||||| ||||| ||||| || ||  | |||||||||||||||||||| |  |  ||||| || ||   |   | |  |     || |  ||   ||   ||||| | |    || |  |||| | || |                 
GGAGTTTGAGAAAGCTTTTAAGATAAAGTTTCCTGCTTGCACGATTGCCGCCAAAAGGCACATTGATTCAAGCACCACGATACTAGATGTTCAAGGCGTGgtatgttgccgttaattgttcctcattgtacgtgcctgtggat-tcctgtgacatggaaaatttatg---ttgtagtttcaacttttag---------------

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag
|||||| ||||  ||||||    | ||||||||  |||| |||||| ||||||||||||| || ||||| || ||||||||| | ||||||||||| |||||| |  || | ||     ||| || |     |||  ||||   ||||   |  ||     | | |||  | || ||                           
GGAGTTTGAGAGGAGCTTTATGATCAAGTTTCCTTCCTGCACTATTTCTGCAAAGAGGCATATTGATTCAAGTACAACTATTCTTGATGTTCAAGGAGTGgtaagtattttcta--cagttcatgatattagttgtgaaatgagtttttttctcatgtgtttatataacttcatattcag------------------------

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|351015523|gb|FQ447352.1|FQ447352
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351026236|gb|FQ428248.1|FQ428248
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|349822502|gb|FQ412766.1|FQ412766
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCCAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351026103|gb|FQ428115.1|FQ428115
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351027625|gb|FQ446789.1|FQ446789
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351055947|gb|FQ453408.1|FQ453408
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|294964977|gb|GW838780.1|GW838780
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|349828849|gb|FQ419182.1|FQ419182
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|161709016|gb|FC058796.1|FC058796
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351040873|gb|FQ438417.1|FQ438417
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|349819344|gb|FQ412238.1|FQ412238
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|349817039|gb|FQ399786.1|FQ399786
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351024179|gb|FQ423602.1|FQ423602
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|30299808|gb|CB976602.1|CB976602
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG
EST: gi|351021812|gb|FQ437197.1|FQ437197
EST:     CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTG                         GGTTTTAAGAATCTAACAAAGGCTGCACGGGAGCTCATTATGCGGCTGCAG
genomic: CAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttc ... aattttccagGGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTCGAGAAAAGCTTTGCCCTAAAGTTTCCAGCCTGTACTATTGCTGCAAAGAGGCACATAGATTCCAGCACAACTATTTTGGATGTTCAAGGCGTGgtatgctttctgtaattttttcttggtcaccattgcaaaatatattttggcccaatcaaaatgtttaaacttatcttttctatttctgatcatcaattttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG