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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT

Basic information

species Vitis vinifera
transcript Vv05s0020g03880.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G701689_T01 (Zea mays), 3'ss of exon 5
--tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgtt-ttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
   |     | |||| ||           | ||| |      ||||   |  | | || | |  ||  | |||     | |  ||||       |||||||||||||||||| || ||||||||||| ||||| |||   ||||| ||||| ||    |  ||  | ||||| |  | ||||   || ||||||||  | || 
agggagaagggatctgtgttctatttctggcaaact---gtctttacactgatacattgtctgatttctgttacatgataaatttttgcttaatttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTATGAACAACCAGAGTCATACGGAAACTGTTCTATCTACG

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G322090_T01 (Zea mays), 3'ss of exon 6
-tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgac--cttttaagctt--cttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
  |     | |||| |        |   | ||  |   |  ||||   |  |   ||  || | |||  | | |  |||    ||||  ||||   |||||||||||||||||| || ||||||||||| ||||| |||   ||||| ||||| ||    |  ||    ||||| |  | ||||   || || |||||  | || 
gggagaaaggatctgtagtatattcctggcaagct---atctttacactgatagatt--gtctcgtttctgttacatgataatttttttgcttaatttcatgcagTTACTGTGAGTGTTTTGCTGCTGGAGTCTATTGTTCTGAGCCTTGTTCGTGTATCGGCTGTCAGAACAACCAGAGTCATATGGAAACAGTTCTGTCTACA

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G00920.1 (Glycine max), 3'ss of exon 7
tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
||| |||      |  | |      ||  ||||   | ||   |  | |  ||  | | |||   | |  | |||| |  |||    ||| ||    |||||| ||||| |||||||||||||||||||||||  |||| || || || || || || ||||| |||||||||||||||||||| |||||||||  ||||
tgtttttattcaatgcaagctttggaaccaaaaaagggaaagaaaatgacctcactgtatttgaatatacttattttatttttctttctttttgtatcagTTATTGTGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G44670.2 (Glycine max), 3'ss of exon 5
--tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
     ||||  | |    |  |||  |    |  |    |   |  ||  | ||     ||||||   |||||  |||    || |   ||| ||    |||||| || || |||||||||||||||||||||||  |||| || || || || || || ||||| |||||||||||||||||||| |||||||||  ||||
gaaagctttagaaccaaaaaagggaaaggaaatgacctcactgtatttgaaattagccttgttttacacttat--tttctttttcttttctttttgtatcagTTATTGCGAGTGCTTTGCTGCTGGTGTCTACTGCATAGAACCCTGCTCCTGTCAGGATTGCTTCAACAAACCTATTCATGAAGACACTGTTCTTCAAACT

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G39080.1 (Glycine max), 3'ss of exon 11
tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
  ||||   |  ||      |      | | | |        |      ||         |  |   |||| || |  |   |||| ||| || |  |||||| ||||| |||||||||||||| ||||||||  |||| || ||| ||||||| || ||||| || |||||||||||||  || |||||||||  ||||
aatcttctcaatttccttcagctttgtgcatattctcttgcatgaaagcttgagaagaaataaggctttattatctttctaattaatcttttttaaccagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCATGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G28740.1 (Glycine max), 3'ss of exon 10
tgtctttgaatctttgagg--ggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
  |||     || || ||    | ||| |      |   | |  |    | ||         |  |   |||| || |      |||| ||| ||    |||||| ||||| |||||||||||||| ||||||||  |||| || ||| ||||||  || ||||| || |||||||||||||  || |||||||||  ||||
cttctcaatttccttcagctttgtgcataatttgttctcatacatgaaatcttgagaataaataaggctttattatctttttaattaatctttttac--cagTTATTGTGAGTGCTTTGCTGCTGGAGTCTACTGCATAGAACCTTGTGCATGCCGCGATTGCTTCAATAAACCTATTCATGTTGAGACTGTTCTTCAAACT

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------tgtctttgaatct--ttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
              | | | ||||  || |      |      ||| || |||   | |  ||| ||||    |   |    ||  ||||||    |    |||||  ||||||||||||||||||||||||||||| || || ||  ||||||||||||||||   ||| ||||| ||||||||||| |||||||| |||||| | || || 
gtaagctcataccccctagcatctcgttaattcctacctgttcaaaataaaaa---actgaattgccttgaagtagttaaccattgtttgactccct---tttctttctgcagTTACTGTGAATGCTTTGCTGCTGGGGTTTATTGCATAGAGCCATGTTCATGTATAGATTGCTTCAACAAACCTATCCATGAAGAAACTGTTTTGGCTACC

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 4
tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttga--ccttttaagcttct-tcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
                  |   ||     |     | |  |||  | | |  || |         | |  || |||||  | | | | | || | |  ||||||||||||||||||||||||||||| ||||| ||  ||||||||||||||||   ||| ||||| || |||||||| ||||||||   ||| || || |||
------------------gtaagctccaaagttccacatttttgatctttggcccttcaaaaaagtttggtgttttgagtcttctgatgtttgtgtggtgcagTTACTGTGAATGCTTTGCTGCTGGAGTCTATTGCATAGAGCCATGTTCATGTATAGACTGCTTCAATAAACCTATCCATGAAGACGTTGTCCTGGCGACT

upper sequence: Vv05s0020g03880.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtctttgaatctttgaggggggcaaaggaaaattagaaat--ttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
                      | ||    ||   |  |||  ||   ||  ||     |  ||| || ||  | | |    |  |  | |||    |||||||||||||||||||||||||||||  | || ||  ||||||||||||||||   | | ||||| ||||||||||| ||| |||||  ||| || || |||
----------------------gtaagttgaatacaccaatctttggcttgctttgaagtagttttttgttgag-tctcttgtactgtgtttccctctgcagTTACTGTGAATGCTTTGCTGCTGGATTTTATTGCATAGAGCCATGTTCATGTATAAATTGCTTCAACAAACCTATCCATAAAGATGTTGTCCTGGCTACT

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|110702530|gb|EE081350.1|EE081350
EST:     ACTGAGGGCTGCAAGCGCTGTAACTGCAAGAAATCTAAATGCTTGAAGCT                         TTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATG
genomic: ACTGAGGGCTGCAAGCGCTGTAACTGCAAGAAATCTAAATGCTTGAAGCTgtaagtcctt ... cttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATG
EST: gi|351044072|gb|FQ452745.1|FQ452745
EST:     ACTGAGGGCTGCAAGCGCTGTAACTGCAAGAAATCTAAATGCTTGAAGCT                         TTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATG
genomic: ACTGAGGGCTGCAAGCGCTGTAACTGCAAGAAATCTAAATGCTTGAAGCTgtaagtcctt ... cttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT
                           atttgac  putative branch site (score: 4)
                                          cttcttcat  putative PPT
                      ttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttgaatctttgaggggggcaaaggaaaattagaaatttattttatttccttctgttttgttcttatgatttgaccttttaagcttcttcatgcagTTACTGTGAATGCTTTGCTGCTGGTGTCTACTGTGTAGAGCCATGTTCATGCCAAGAATGCTTTAACAAACCTATTCATGAAGATACTGTTCTTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - agggggg
- - - - - - - - - - - - - -ggaaaat