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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC

Basic information

species Vitis vinifera
transcript Vv13s0019g03880.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g09450.1 (Oryza sativa), 3'ss of exon 2
caactaatgc--ctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtt--tgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
    |||| |  | ||  || |   || |  |  || ||     | |  || | |||  ||| |  || ||     |     |||  |  | ||        ||||| || ||   | | || ||||| || || || |||| || ||||||||| || |||||||| |||||||| ||||| |||||||||||||| || |||
---ttaattcaacagtttttatttggtaacttg-caatttgagatttatttacgtttctttctttcattaagttgttgttcctttcctcctttgatccctgcagGGAAAACGCCCATCCTGAGAAGGTAAAAGAGGCGCATAAGAAGGTCATGGTTGCTAACCATCCAGATGCAGGCGGTAGCCATTACCTTGCTTCAAAGATC

upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g06454.1 (Oryza sativa), 3'ss of exon 2
caactaatgcc-tgtcattttgaagtcat--gtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
    |  ||   | |||  |||   |  |   |||    | ||   |  |  | |  ||||| ||||         ||     |||  || ||        || || ||||    | | || ||||| || || ||||| |  | ||||||||| || || ||||| |||||||| || ||||||||||||||||| || || 
--gttggtgatgtttcaacttgtcattgttaatattcaatttgaggc-acactatgattcttgctattgttcattggtctcttttttcttttgatgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGTTGCCAATCATCCGGATGCAGGGGGCAGTCATTACCTTGCTTCGAAGATT

upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G040587_T01 (Zea mays), 3'ss of exon 3
---caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggt-ttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
   | | |   | | |||||| |  |||  | ||| |||   ||  ||||||  |  ||   | | | |    || |  |   | |  || | | | ||   ||||| | ||| |  ||||| ||||| || || || || | |||||| ||||| || |||||||| ||||| ||||| |||||||||||||| || || || 
gtactagtgtggtcagtcattcttgagtttt-tataagt---gtcgctgcttagtgattaaacgtttttttttcatgctagcttataattattgatgtttccagGGAAACTGCCAACGCAGAGAAGGTAAAAGAGGCGCACAAGAGGGTTATGGTCGCCAACCATCCAGATGCTGGTGGAAGTCATTACCTTGCGTCAAAGATT

upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G16850.1 (Glycine max), 3'ss of exon 2
--caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
    ||||     |||  ||| |           | |   ||||  |  | ||||| || ||     |     || | | |  |||||    | ||    ||||| ||||| ||||||||||||||||||||||||||||| | ||| ||||| ||||||||||||||||| ||||| |||||||| |||||||||||||| 
tattactaggttgtgtgctttagcttctccaagactggaatgttgatcttgtctttgtcatcaagcttttctgaatttata--ttgttccatgattcatcagGGAAAATGCAACTGCAGACAAGGTGAAGGAAGCACATAGAAAGGTTATGGTTGCAAACCATCCTGATGCGGGTGGAAGTCATTATCTTGCTTCCAAAATA

upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G23760.1 (Glycine max), 3'ss of exon 1
--caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC---
    ||||   | |||  |||||           | |   ||||  |  | ||||| || |      |     || | |    |||||    | ||    ||||| ||||| ||||| ||||||||||||||||||||||| ||||| ||||| ||||||||||  | || | ||  |  |    |  |      ||||  |   
tattactaggccttgtacttttgctcctccaagactggaatgttgatcttgtctttgtcgtgaagcttttctaaatttatg--ttgttccatgattcatcagGGAAAATGCAACTGCTGACAAGGTGAAGGAAGCACATAGAAGGGTTATGGTTGCAAACCATCTGGGTGGAAGTCTTGCTTCCAAAATAAA---CAAAGCCAAA

upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G35795.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------caactaatgcct-gtcattttgaagtcatgta---tcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgttt-----gtggg--tttg-----------atagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
                                  ||  ||  | ||  |||   | || |  |   ||| ||  |||   || ||    |  || | || ||||  ||||  ||  ||||||     |||||  ||||           | ||||||| ||   | || || ||||||||||||||||| |||| ||| ||||| ||||||||||| |||||||||||||| |||| ||| || || || |||
gtgaaggaaacacacacacatactctctctttctcttgtgtttagtagtttctcaatcctcaatgatcaatttggttatagcattagcatagtttccat-tgaagaaagtgtaacgttgtttgaaatgtggggttttgtgattgaaaacacagGGAGAGTGTAGCGGCGGAAAAGGTGAAGGAAGCACACAGGAAGGTAATGGTAGCAAACCATCCAGATGCAGGTGGTAGCCATTTCCTAGCCTCTAAGATC

upper sequence: Vv13s0019g03880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G09700.1 (Arabidopsis thaliana), 3'ss of exon 2
caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgg-gtttga-tagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
 |  |  |  |       |  | |   || ||  |||  ||    | |||       ||  |||  |     |  |     |   |||||| |||||| |||||||| ||   | ||||| |||||||||||||| ||  | || || |||||||| || ||||| |||||||| || || ||||||||||| || || |||
tatgttcttacacaagggtaaatggtttgcatatgtttagtggtggtttttgcgacattattat--ggcttgatgagtttgtcacttgtggtgtttgaatagGGAGAGTGTAGCGGCAGAGAAGGTGAAGGAAGCTCACCGTAGAGTGATGGTGGCTAATCATCCAGATGCAGGAGGAAGCCATTACCTTGCGTCTAAGATC

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|77587989|gb|DV223198.1|DV223198
EST:     TTCCAGCCTACAATGACAAAAAGGGAAGCAGCTCTTATTCTTGGCATTAG                         GGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGT
genomic: TTCCAGCCTACAATGACAAAAAGGGAAGCAGCTCTTATTCTTGGCATTAGgtaccactaa ... ggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGT
EST: gi|71869973|gb|DT019028.1|DT019028
EST:     TTCCAGCCTACAATGACAAAAAGGGAAGCAGCTCTTATTCTTGGCATTAG                         GGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGT
genomic: TTCCAGCCTACAATGACAAAAAGGGAAGCAGCTCTTATTCTTGGCATTAGgtaccactaa ... ggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC
                          aagtaaaaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caactaatgcctgtcattttgaagtcatgtatcagttctgtttctgctttctttttcttcctatatgaaccaagtaaaaatttgtttgtgggtttgatagGGAGAATGCGACTGCAGACAAGGTGAAGGAAGCACATAGGAGGGTCATGGTGGCAAACCATCCTGATGCAGGTGGTAGTCATTACCTTGCTTCCAAAATC

- - taatgcc
- - - - - - - - - - - - tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaa