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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgattataataactccaataaaataactaaaag...

Basic information

species Vitis vinifera
transcript Vv02s0025g03530.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 4
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagat-atcctcatattg----attata-ataactccaataaaataactaaaag-------------------------------------------
|||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| ||||| |||||| |   || |     |||   | | ||||||  || ||   ||  |  ||   || ||      ||||       ||| ||| || || |   | |  |                                                
AAGCATTTCACTAGAACCTGGTGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgcgcactgcatccctgtattaacttcttgctttatg--tgattttcagttatgatttgtgcattgccatgccatatatatcttcagtccgaaagtttttttttttgccagcagttgatccaatccgaaacgtctattcttgtag

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g03820.2 (Oryza sativa), 5'ss of exon 4
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtact-tgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgat--tata-ataactccaataaaataactaaaag---------------------------------------
|||||| ||||| ||||| || ||||||||||| ||||| ||||| ||||||||||| || |||||||| ||||||||||| |||||||| ||||| |||||| | ||   | | || |  | || |  |  | ||||  |   |    ||  | ||| | | |||    ||   ||| ||| || || |   | |  |                                            
AAGCATTTCACTAGAACCTGGCGGTCAGTTTGAACTTAGTGGTGCTCCTCTTGAAACATTACATCAAACTTGTGCTGAGGTCAATTCACATCTTTACCAGgtaatgtgcagtgcatccctgtattaacttcttgctttatttgattttcacttatgatttgcgcattgccatgccatatatatcttcagtccgaaagtttttttgccagcagttgatccaatccgaaacgtctgttcttgtag

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 3
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgattataata--actccaataaaataactaaaag------
|||||||||||| ||||| || || || ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| ||||| || ||||||||||||         |||||| | | |    ||| |  |  | ||    | |  ||  ||   || |  |||  | |  ||  | ||   |   | |  ||| |       
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACATTACATCAAACTTGTGCTGAGGTCAATTCGCATCTTTATCAGgtaa--------cttctcttacattgcattccttgtacagcatcttacagaaactatgatcttagtttgtgtgtgttaccattcttttgtcagagataatacagtacc

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 3
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggatacca-aagatatcctcatat-tgattataataactccaataaaataactaaaag
|||||||||||| ||||| || || || ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| || ||||| || |||||||||  | ||  | |    | | ||| | | | | |          || |  |  |  |   ||| | | || || || |       ||| ||  ||| |   
AAGCATCTCACTAGAACCTGGAGGCCAATTTGAACTTAGTGGCGCTCCTCTCGAAACGTTACATCAAACTTGTGCTGAGGTCAACTCACATCTATATCAGgtaact-tctctttctgacgttttcttttccctgtgcatcttgcagaaattatgatcttagctcgtgtgtgtttttacttgacattatataa-gactgacca

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 4
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttct-ccttcttcatcttct-tctttgatcactggataccaaagatatcctcatattgattataataactccaataaaataactaaaag
 ||||| ||| |||| || |||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| |||||||| ||||||||||||||||||||    ||  | | |    ||| || | | |||   || ||||       || ||  |      ||| ||| |  || ||    ||||  || |  
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTCCCACCTTTATCAGgtacttgtttcgctgatgcataaaccattttttcttttttgccattggagtgatttgaaattttttacgcgatcatattttctacagatgaatatgtata--

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 4
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgattataataactccaataaaataactaaaag-----
 ||||| ||| |||| || |||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| |||||||  ||||||||||||||||||||   |   ||  | | | | ||| || ||||  || | ||       |  ||  | ||    || ||| |  || |    |||||  ||  |      
GAGCATATCATTGGAGCCTGGTGGTCAGTTTGAACTTAGTGGAGCTCCTCTTGAAACCTTGCATCAGACTTGTGCTGAAGTTAATTTGCACCTTTATCAGgtacttgt---ttcgctgatacattaactttttttttg-ccattagagtgatttggaatttttatgc-aatcatattttctacggataaatatgtatcatcattg

upper sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 4
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgattataataactccaataaaataactaaaag
|||||| ||||| ||||| || |||||||| |||||||| ||||| |||||||| |||||||||||||| |||||||| || |||||||| |||||||||||| ||   |   |  |  ||    ||  |||      |  ||  || |   ||   |   || ||  |||  | | |                      
AAGCATTTCACTTGAACCTGGGGGTCAGTTCGAGCTTAGTGGTGCACCTCTTGAGACTTTGCATCAAACTTGTGCTGAAGTCAATTCACATCTTTATCAGgtaatttcaaagataattattgccaatgctctcaccctaaaacgtgacaaataaccaactatc-tacggat-gtcacag---------------------

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|351057110|gb|FQ450817.1|FQ450817
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAAGCA-TTGCAGAGGAAATG
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAA-GCAGTTGCAGAGGAAATG
EST: gi|30300777|gb|CB977571.1|CB977571
EST:     TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349828851|gb|FQ419184.1|FQ419184
EST:     TTGAAACTTTGCATCANACTTGTGCTGAGGTTAATTCACACCGATAACTC                         GTTAAATCAGTTGCATAGGAAACGGGGA
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGA
EST: gi|349809354|gb|FQ401122.1|FQ401122
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349816669|gb|FQ404916.1|FQ404916
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349815261|gb|FQ400416.1|FQ400416
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|71886560|gb|DT035615.1|DT035615
EST:     TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|351042065|gb|FQ456275.1|FQ456275
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|30132095|gb|CB917434.1|CB917434
EST:     TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349808498|gb|FQ405642.1|FQ405642
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTT
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTT-
EST: gi|351012028|gb|FQ429834.1|FQ429834
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349820754|gb|FQ404128.1|FQ404128
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|71885452|gb|DT034507.1|DT034507
EST:     TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|351016353|gb|FQ446213.1|FQ446213
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349810574|gb|FQ402817.1|FQ402817
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCTTAGGTATTGGTTTC
EST: gi|349809614|gb|FQ414504.1|FQ414504
EST:     TTGAAACTTTGCATCAAACTTGTGCTGAGGTTAATTCACACCTTTATCAG                         GTTAAAGCAATTGCAGAGGAAAT
genomic: TTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAAT
EST: gi|161712407|gb|FC061712.1|FC061712
EST:     TGAAACTTTGCATTCAAACCTGTGCTGATGTTAATTCACACCTTTATCAG                         GTTAAAGCAGTTGCCGAGGAAATGGGGATTGGATTCT
genomic: TGAAACTTTGCAT-CAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtca ... tgtttaacagGTTAAAGCAGTTGCAGAGGAAATGGGGATTGGATTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCATCTCACTGGAACCCGGTGGTCAGTTTGAGCTTAGCGGTGCCCCTCTTGAAACTTTGCATCAAACCTGTGCTGAGGTTAATTCACACCTTTATCAGgtacttgtcattcttctccttcttcatcttcttctttgatcactggataccaaagatatcctcatattgattataataactccaataaaataactaaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa