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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG

Basic information

species Vitis vinifera
transcript Vv18s0072g00770.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 5
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttg-cagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
                  | | | |  ||||      | |    ||   | |  ||    | ||  | |   | ||| |   | |    ||  | || ||||||||||| |||||||||| ||| || || || || ||||||||||| || |||||||||||||| || ||||| |||||||| |||
---------------gtaaccatgtcatctgaatccatttccccttcaga-tatatcacatgtac-tctcttcctaaatagacttggttctggtatgacagCTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 6
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
   | | ||  ||| |||   |   ||     |  | ||| ||| |  || |   | |    |   | |  |||      || |    | ||  | |||||||||  | || ||||||| |||||| ||||| || || ||||||||||| || |||||||||||| | ||||| ||| |||| |||
---gtaatc--gacctcctaatccatcc----tactctataaatgtcataat---tctcacctgaatataacctg-----tgtaactaatttgat-gcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 5
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
   | | |    | ||   ||| ||   |   | || |   ||   |||| | ||| | |         |   | |  |  |||    |  |  | |||||| ||  | ||||||||||||||||| ||||| || || || || || |||||||||||||||||||| || || ||| |||| |||
---gtaataaccaattaattctcttgaacccatcttctccgaa---ggtaat-catctgtaacgaaatataattgacatgcgcaaccaatctgat-gcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCACTTGGGGAGTTCATACTAACCCATCCAGACATCAAG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 7
tctgcagtctagacttccatctttttctctgg-tgttgtattaatttggtactgcatttattttaggtgttgcctt--aattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
     |   |    | |     | | |   |  |||||  || ||||   |||  |      |||  |  ||  ||  ||||| | ||   |   |||||||||||||||||||||||||| | ||||||||||| || |||||||| ||||| ||||| |||||||| || |||||||| |||||||||
--aataacattttttcctggtatatccaaggactgttgacttcattttaaact-tacaatgcttaattactggattacaatttggtatgtaatggatttgcagCTTGTGTTAAGCACTGGAGCAGGTGTTAATGGTTTCACCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAG

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S385_43V6.1 (Physcomitrella patens), 3'ss of exon 6
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactg--catttat-tttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
      | |||| | |||||||| |    |          |||| ||||   |   | |  |  ||   |   | || | |       |   ||   |||||| | ||  | ||||| ||  |||| |||||||| || ||||| ||||| |||||||||||||||||  | || |||||  |||| |||
---tttgcctagtcatccatcttatcgaatttgcaccagctaatctggtggaggttagtagtgcttgcctagagtctcagtaacaaggttgtctgtattgcagTTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAG

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|38516542|gb|CF983717.1|CF983717
EST:     GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAAACTGGTGTTAATGGATTTACCCTTGATCCCAT
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAA-CTGGTGTTAATGGATTTACCCTTGATCC-AT
EST: gi|32247391|gb|CD713210.1|CD713210
EST:     GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
EST: gi|32271549|gb|CD720708.1|CD720708
EST:     GAAAGAATATGGTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
EST: gi|32267853|gb|CD717012.1|CD717012
EST:     GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
EST: gi|32270796|gb|CD719955.1|CD719955
EST:     GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
EST: gi|110361485|gb|EC924959.1|EC924959
EST:     GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
EST: gi|30324923|gb|CD008185.1|CD008185
EST:     GAAAGAATATGTGGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
EST: gi|32270921|gb|CD720080.1|CD720080
EST:     GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACG                         CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA
genomic: GAAAGAATATGTTGGCAGCTGGTTATTGCATGTATGGAAGCTCTTGCACGgtacaaagga ... ttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG
                          ccttaat  putative branch site (score: 4)
                                            cttattt  putative PPT
                            ttaattttgcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgcagtctagacttccatctttttctctggtgttgtattaatttggtactgcatttattttaggtgttgccttaattttgcattacacttatttgcagCTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG

tctgcag
- - - - - - acttcca
- - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca