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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggacttcttctttcaatttggtttctctttatattactctgaacattaacattccctgattgtgtcattactgttttgatggcccgtcttatacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA

Basic information

species Vitis vinifera
transcript Vv11s0016g03200.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 7
---------------------------------------------ggacttcttcttt--caatttggtttctctttatattactctgaacat-taacattccctgattgtgtcattactg------ttttgatggcccgtcttatacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA
                                              || ||||   ||  || | |    |     | ||| | ||  ||  | |   |   |||          ||| ||       ||  |||      ||     ||||||||  ||||| || |||||||| |||||||| || || ||||| ||||||||||||| 
gtgagcttgctaatctaatcacttagcaatatttatgccaaattctgatttctgtgttggcagtataaaattgggatgtatcaatcataaggtattctacggcctatgccaactgttagtgaagatccttacatgttttccctctattttccagAGGTTTTATTGTCAATCTTGGCGATATGCTCGAACGGTGGAGTAACTGTATTTTCAG

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G01170.2 (Glycine max), 3'ss of exon 7
------ggacttcttctttcaatttggtttctctttatattactctgaacattaacattccctga-ttgtgtcattactgttttgatggcccgtcttatacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA
      |||  | |   | | | | | | |    ||   ||||  |   |||   | |  ||||| || |  |||||    |||||  |   || ||||  || |||||| || ||||||||||||||||| |||||||||||||||||||||||| |||| ||
aggtaaggaagtatctatgctactagatcttaactt-cgttacctttgtcatgcccttctcctgaattattacatta----tttgactgattgt-ttatg-ttgcagAGCATTCATAGTGAATCTTGGTGACATGCTGGAGCGCTGGAGCAACTGTGTTTTTAA

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G08470.1 (Glycine max), 3'ss of exon 7
ggacttcttctttcaatttggtttctctttatattactctgaacattaacattccctga-ttgtgtcattactgttttgatggcccgtcttatac--ttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA
  |   | | |   |   | |||  |   |  |||||  |   |||   | |  ||||| || |   || | |    ||||      | || |    || |||||| || ||||||||||||||||| |||||||||||||||||||||||  |||| ||
-aagaacctatgcta--ctagttcttaacttcattacctttgtcatgcccttctcctgaattattatataatttgactgattattgatgttgttatgttgcagAGCATTCATAGTGAATCTTGGTGACATGCTGGAGCGCTGGAGCAACTGCGTTTTTAA

upper sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G35190.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------ggacttcttctttcaatttggtttctctttatattactctgaacat-taacattccctgattgtgtcattactgttttgatg-gcccgtcttatacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA
                            |   |||     || |||     |    ||||||       | ||| | | |     |  |  | |    | || || |||       | || |   | |||||| ||||||||||||||||| ||||||||||| || ||||||||  |  |||| ||
gtataacgaacaacctttcttatcgttcgtttttccatcatctattaaaccttgaattatatattgactagcatctgatacatattagtattttgtcaattggttggatttatttattttctgtctacagAGCATTTATAGTGAATCTTGGCGATATGCTGGAACGTTGGAGCAATGGCTTTTTTAA

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|32459007|gb|CD800181.1|CD800181
EST:     TCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGT
genomic: TCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCG-TT-TATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGT
EST: gi|110727031|gb|EE103356.1|EE103356
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|45771236|gb|CN007088.1|CN007088
EST:     GATAAGGACGCTAGACTTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|83275538|gb|DV939546.1|DV939546
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTCGGTGATATGCTGGAGCGCTGGAGCACCTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|110428851|gb|EC995334.1|EC995334
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|83276122|gb|DV940130.1|DV940130
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|110390246|gb|EC955146.1|EC955146
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|30253347|gb|CB970898.1|CB970898
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|71887181|gb|DT036236.1|DT036236
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|77589174|gb|DV223847.1|DV223847
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|83275983|gb|DV939991.1|DV939991
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|71884795|gb|DT033850.1|DT033850
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|30253270|gb|CB970821.1|CB970821
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|110421097|gb|EC987385.1|EC987385
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
EST: gi|71884047|gb|DT033102.1|DT033102
EST:     GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGG                         AGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT
genomic: GATAAGGACGCTAGACCTCAGACATGGGAATATGTAGCGCCATTAAAAGGgtgagtaatt ... atacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacattccctgattgtgtcattactgttttgatggcccgtcttatacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA
                                              tacttcc  CT-rich tract
                                           ttatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggacttcttctttcaatttggtttctctttatattactctgaacattaacattccctgattgtgtcattactgttttgatggcccgtcttatacttccagAGCGTTTATAGTGAATCTTGGTGATATGCTGGAGCGCTGGAGCAACTGTATTTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- -cttcttc
- - - - - - - - - - - - - - - - - - ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggcc