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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttacccaattataaactcaaaaaaaaaaaaaatgtgttggtaggacctctgttaagtgtcagaaaaaaggcctttatgtcatggttcatgtttacttccagtaatttgtcttggcattcatatgagattggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATTTCAAATGCAGGCTTGGAGGCTTCTCAAATTGATTACTATGAAATAAATG

Basic information

species Vitis vinifera
transcript Vv12s0057g01200.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 9
gtacttacccaattataaactcaaaaaaaaaaaaaatgtgttggtaggacctctgttaagtgtcagaaaaaaggcctttat----gtcatggttcatgtttacttc--cagtaatttgtcttggcattcatatgagattg-gcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATTTCAAATGCAGGCTTGGAGGCTTCTCAAATTGATTACTATGAAATAAATG
|||| ||   || ||||   |   ||| |  ||  |  | ||   |  |       ||||    ||||||||    |||||     | ||   |  |||||  |     | || | |   ||   ||||||||||| ||| ||  |||||| |||||| |||||||| ||||||||| ||||||| ||||| ||||||||| | || ||||| |||||| |||| ||||||||||  |||||||| ||||
gtacata---aaatatatttt---aaatatgaactacatcttcagactataaaaaataagaagtagaaaaaatcattttattcacattatttctagtgtttgatgtattattagtataatttcatattcatatgaggttgagctgtgcagGAACCAGAGTTATTTACAACAGCTCCATCCCTTGCCATTCCCAAAGCTATTGCCAAGGCAGGGTTGGAGACTTCGCAAATTGATTTTTATGAAATTAATG
















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|352790687|gb|FQ475445.1|FQ475445
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCCGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|30130059|gb|CB915398.1|CB915398
EST:     TGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|30133903|gb|CB919242.1|CB919242
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGNCA-TTCCAAAAGCTAT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTG-CAATTCCAAAAGCTAT
EST: gi|71876405|gb|DT025460.1|DT025460
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110699364|gb|EE076300.1|EE076300
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCANGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCCTC-AGCCCTTGCNATTCCAAAAGCTAT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGC-TCCAGCCCTTGCAATTCCAAAAGCTAT
EST: gi|30129594|gb|CB914933.1|CB914933
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110700654|gb|EE077500.1|EE077500
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAAAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|30254555|gb|CB971300.1|CB971300
EST:     TGGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTAT
genomic: TGGG-CTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACC-AGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTAT
EST: gi|30129595|gb|CB914934.1|CB914934
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAN                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|349833317|gb|FQ416695.1|FQ416695
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110368276|gb|EC932247.1|EC932247
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110371396|gb|EC935385.1|EC935385
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|27584750|gb|CB007445.1|CB007445
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|33402805|gb|CF208432.1|CF208432
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110361968|gb|EC925474.1|EC925474
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|30133750|gb|CB919089.1|CB919089
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110361336|gb|EC924802.1|EC924802
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110362059|gb|EC925566.1|EC925566
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGTTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110357331|gb|EC920800.1|EC920800
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|32246227|gb|CD712046.1|CD712046
EST:     CAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: CAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|33403297|gb|CF208924.1|CF208924
EST:     TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
EST: gi|110723122|gb|EE100072.1|EE100072
EST:     TTGGGCTGTCAGTCATTGCCAAGATTGCAGGATACGCTGATGCTGCTCAG                         GCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT
genomic: TTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAGgtacttaccc ... ggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtttacttccagtaatttgtcttggcattcatatgagattggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATTTCAAATGCAGGCTTGGAGGCTTCTCAAATTGATTACTATGAAATAAATG
               agtaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttacccaattataaactcaaaaaaaaaaaaaatgtgttggtaggacctctgttaagtgtcagaaaaaaggcctttatgtcatggttcatgtttacttccagtaatttgtcttggcattcatatgagattggcattgcagGCACCAGAATTATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATTTCAAATGCAGGCTTGGAGGCTTCTCAAATTGATTACTATGAAATAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG