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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacttggactatagttatttccattgatacctttactttcatattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG

Basic information

species Vitis vinifera
transcript Vv09s0054g00010.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 2
----gtatgcacttggactata--gttat--ttccattga-tacctttactttcatattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG
    | |  |||||    | ||  |||||  |  || ||| ||    |  |    |  |  |||  || | || ||        | ||||     |  ||||||||||| |||||||||||||| || |||||||||||||||||||||||||| |||
gtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgtta--caaatctgttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG

upper sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G178807_T03 (Zea mays), 3'ss of exon 3
gtatgcacttggactatagttat-ttccattgatacctttactttcatattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG------------------------------------------
              ||| | | | | ||| || |  ||    ||   |    ||  ||  ||  | | |  |||  | | ||     |  ||||||||||| |||||||| |||||  | ||||| ||||||||| |||||||||| |||                                          
-------------gtatggctctgtcccaatggttgct--gattcagttgctatgctcaagtgttgactgttgtcaaatgtgctgtgt--agTATCAATGCCATGCACCCCAAGACCCGCAAGATCTTGCAGCTCCTGCGTTTGAGGCAGATCTTCAATGGTGTCTTTCTCAAGGTTAACAAGGCAACTATT

upper sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 3
gtatgcacttggactatagttatttccattgatacctttactttcatattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG
         ||      |  |  ||       ||  | |        |||  |||  |  | ||  ||  |  |  |  || ||||  |||||||||||| ||||| || ||||| || ||||| ||||||||  |||||||||| |||
--------gtgagtcgcaagtgcttatgccagtat-tatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaacta-cagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG

upper sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgcacttggactatagttatttccattgatacctttactttca-tattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG
|||||   |     | | |||  |   ||    |  | ||    || | |  || || | ||||| ||   |  |   | |  |  || |||||||||||| ||  |||| ||||| |  |||||| | |||||||||||||||||||||
gtatgttatactgttgttgtttgtcttataagcatttctaaagccagtgtctatgttgttgttcttatctgttgttctttttaatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG

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|161719010|gb|FC067630.1|FC067630
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTTG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|33408299|gb|CF213926.1|CF213926
EST:     TATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|351030969|gb|FQ439005.1|FQ439005
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110427908|gb|EC994363.1|EC994363
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110362548|gb|EC926091.1|EC926091
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|71865492|gb|DT014547.1|DT014547
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|77588453|gb|DV223438.1|DV223438
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110686521|gb|EE064257.1|EE064257
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|71870639|gb|DT019694.1|DT019694
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|33408211|gb|CF213838.1|CF213838
EST:     CGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: CGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|71873389|gb|DT022444.1|DT022444
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110362206|gb|EC925723.1|EC925723
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110360464|gb|EC923584.1|EC923584
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|161716946|gb|FC068826.1|FC068826
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110364696|gb|EC928138.1|EC928138
EST:     CCAGAGGCTAAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCCCCCAAAGACGAGAAAGATTTTGCAGCTCTTGGCGTT
genomic: CCAGAGGCT-AAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTT-GCGTT
EST: gi|71873570|gb|DT022625.1|DT022625
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|161719477|gb|FC067687.1|FC067687
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|71873637|gb|DT022692.1|DT022692
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110387232|gb|EC951884.1|EC951884
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|161714799|gb|FC063247.1|FC063247
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
EST: gi|110365131|gb|EC928904.1|EC928904
EST:     TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGG                         TATCAATGCTATGCACCCAAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT
genomic: TTTTACGTTGACCCAGAGGCTAAACTTCTATTTATGATTCGTATCCGTGGgtatgcactt ... gaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttcatattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG
          tattaat  putative branch site (score: 2)
                                                ctttc  putative PPT
     tttcatattaatattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcacttggactatagttatttccattgatacctttactttcatattaatattctggttctcattcctgttcactctggaactttcagTATCAATGCTATGCACCCGAAGACGAGAAAGATTTTGCAGCTCTTGCGTTTGAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC