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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctttataaacattattatgttggcctatattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA

Basic information

species Vitis vinifera
transcript Vv18s0072g00120.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g40710.1 (Oryza sativa), 3'ss of exon 1
tcctttataaacattattatgttggcctatatt-aatgtatttcttcatcagccaa--tctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
     || || ||   | |  | | | ||  ||   ||| ||  |  ||  |  ||  | |   |  |||||   |    |     ||    |  |    ||||||||| ||||| || ||||| || ||||||||||||||||||||||| ||||| || |||||| | ||||| |||||||||||||||||||||||||| 
---aataaaagcagggtgacctagacttaggttcggtgttttgttgaatagggtaagatttgcttgtttactaatggtgattctgatcatcaaaatctcgcagATGGGCTATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACCGGCTCGGATTTTGTTCAACAAGTGAAGATCCTTCTCTCCAATTTTGGGATT

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G143469_T01 (Zea mays), 3'ss of exon 1
--tcctttataaacat-tattatgttggcctatattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
  | |   ||    |  |   | | |   | |  ||  ||  |   || |  |   |    | ||   | |     |   ||    |     |       ||| ||||| ||||| || ||||| || |||||||||||||||||||||||||||||||| |||||| | ||| | ||||||||||| |||||||| || || 
aatacacgatgggtagatgcaaagattcaccacgttcttgagtaggttaagga---agctcatctctatgcgctaattcatcagctttctacaaaccttgcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACAGGCTCTGATTTTGTTCAGCAATTGAAGATCCTTCTTTCCAATTTCGGAATT

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G019807_T01 (Zea mays), 3'ss of exon 1
tcctttataaacattat-tatgttggcctata---ttaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctg--ggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
      | |||    |  || || | | ||     | |     ||  |   |  |  ||   ||||| |  ||  |  ||   ||    ||    |  |    ||| ||||| ||||| || ||||| || ||||||||||||||||| ||||||||||| || |||||| | ||| | ||||||||||||||||||||||| || 
------aaaaatgcaagataggtagacgtaaggattcaccacgttgttgagtacgttaagacagcttgtctctatgcgctaattcaccttgctacacatcttgcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTATGCAACAGGCTCGGATTTTGTTCAGCAAATGAAGATCCTTCTCTCCAATTTTGGAATT

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G08740.1 (Glycine max), 3'ss of exon 1
tcctttataaacattattatgttggcctatattaatgtatttct-tcatcagccaatctagcttcttacttgggtctgtctctgtctgggatg--ttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
  | |  ||   |||       || |  |  | | || ||  |  |  |    |||  |    | | | || |   |     | | |    |   ||   ||||||||||||||| ||||||||||||||| ||||||||||||| |||||||| || ||||||||||||||||||||||||||||| || |||||||| |||
--catcctatttattgcatacctgtcacacttaattgaatccccattgttgtgcaagttctgatgt-attttgacttactaatatgtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTTGGGTTGCTAACAGAGTATGCAACAGGTTCGGACTTTGTTGATCAAGTAAAGATCCTTCTATCGAATTTTGGAATA

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G27850.1 (Glycine max), 3'ss of exon 1
-tcctttataaacattattatgttggcctatattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaat----cagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
 |  | |  ||    |  || |||      | ||  | |||||  ||    || | |   |||   || || |   |       || |  || | | |    ||||||||||||||| ||||||||||| ||| ||||||||||||| |||||||| || ||||||||||||||||| ||||||||||| || ||||||||||||
ttgttgtgcaagttctgcta-gttttttattttttttttattttatcggttgcaagttctgctg--tattttgacttacta--atcagtaatttcatttctacagATGGGCAATGTTTGGTTTTGCTGTAGGGTTGCTAACAGAGTATGCAACAGGTTCAGACTTTGTTGATCAAGTGAAGATCCTTCTATCGAATTTTGGGATA

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G36650.1 (Glycine max), 3'ss of exon 1
tcctttataa-acattattatgttggccta-tattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaat----cagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
   ||||| | || |||   | ||     | |||     ||||| | |     |   |||  ||| ||| |||  | |   |   ||||| || ||  |    ||||||||||||||| ||||||||||||||  ||||||||||||| ||||| || || || ||||||||||||||||||||||||||||| |||||||| |||
---tttatgacaccttagctttttcatggaatatgtgcatatttatgctagttctgctctgcctttttatttgacttt---ttaatctggaattttgtttcaacagATGGGCAATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACGGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTCTCGAATTTTGGAATA

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G30940.1 (Glycine max), 3'ss of exon 1
------tcctttataaacattattatgttggcctata-ttaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
      | | |||      | |||   |  |   ||| | ||||    |  |  || ||| || ||  |   |  ||   ||||    | | |      || | ||||||||| ||||| ||||||||||||||  ||||||||||||| |||||||| || || |||||||||||||||||||||||||| || ||||||||||||
atatgataccttagttgtttcattgaatatgtgcatactcaatgctagttctgctctgcctatttatttgactttttaa-tctggacttttgt------ttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA

upper sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G34000.1 (Arabidopsis thaliana), 3'ss of exon 1
tcctttataaacattattatgttggcctatattaa-tgtatttcttcatcagccaatc--tagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
   || ||     ||   ||   | | |||||    |  | ||   ||   | || |   ||    ||      |   |  |||||| ||   ||||  | || ||||| ||||| ||||| || ||||| ||||| |||||||| |||||||| || ||| ||||||||||||| |||||||||||||| ||||| || || 
--attgatgtttcttcaaattcagacatatatagcctaaagtttcacacttgtcagttggtactgcctagacaagagataactctgtgtgttttgtttgt-agGTGGGCTATGTTTGGTTTCGCAGTTGGTATGCTCACAGAGTATGCAACAGGATCAGACCTTGTTGATCAAGTTAAGATCCTTCTCTCAAATTTCGGCATT

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|110373096|gb|EC937306.1|EC937306
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAG                         ATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAGgtacatgatg ... tgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
EST: gi|110418313|gb|EC984458.1|EC984458
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAG                         ATGGGCAATGTTCGGTTTTGCTGTTGTGATGCTAACAGAGTACGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAGgtacatgatg ... tgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
EST: gi|46919203|gb|CN548532.1|CN548532
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAG                         ATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAGgtacatgatg ... tgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
EST: gi|110366292|gb|EC930113.1|EC930113
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAG                         ATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAGgtacatgatg ... tgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
EST: gi|110421337|gb|EC987633.1|EC987633
EST:     CAAGAATGAGATTTCCAATGGAAG                         ATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
genomic: CAAGAATGAGATTTCCAATGGAAGgtacatgatg ... tgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
EST: gi|110428261|gb|EC994727.1|EC994727
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAG                         ATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAGAATGAGATTTCCAATGGAAGgtacatgatg ... tgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA
                ttcttac  putative branch site (score: 2)
                                            atgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctttataaacattattatgttggcctatattaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA

- - - ataaaca
- - - - - - - - - -tgttggc
- - - - - - - - - - - - - - - - - - - - - - - - - gccaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctgg