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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 2
ttttttggggattcaaaggggatt--ttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
  |||||    |   |     |||  ||  || || |  ||  |||||||   |  ||| |||   | || || ||| ||||||||||||||| |||||||||||||| |||||||| |||||||||||| | || || ||| | ||||| ||||||||  ||||||| || |||||||  || |||||  | |||||||| 
--ttttgcttttatgactaaaattaattatttgttacctaattttttcttctgttctttttttaaaaaaaattgtagcttctttatctttgagaaaatgcagGTATGTCGGGAACATCCATACGCAGGTAACTGAGCCGCTTTTGCAAGAAGTTTTTGCGGGTACTGGCCCAGTTGAAGCTTGTAAGCTTATCAGAAAGGAT

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 2
---ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
   |  |||   || | |||       || ||| || |  ||  ||||  || |  | || |||| || || || ||| ||||||||||||||| ||||||||||||||||||||||| ||||| |||||| | || || ||| | ||||| |||||  |  ||||||| || |||||||| || |||||  | |||||||| 
ttttgctttaatgactaaaattaa---ttacttgttccctaatttttttcttctgttctttttttttaaaaattgtagcttctttatctttgagaaaatgcagGTATGTTGGGAACATCCATACACAGGTAACTGAGCCGCTTTTGCAAGAAGTTTTCTCGGGTACTGGCCCAGTTGAAGGTTGTAAGCTTATCAGAAAGGAT

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 2
-----ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
     ||||||    |||  ||  || ||||| || || ||   || |||  |           |||| |    | || |||  ||||| |||       |||||||||| ||| |||||||||||||||||  | ||    |||||||||||| |||||||||||||||||||| ||||| |||| || ||| | |||||||| 
gtgagtttttt----atttcaattggtttttctttctttctttcgcctttggtataatgcagagtttcaatttgtaattgttcttttatgttt-------tgcagGTATGCTGGAAACATTCATACGCAGGTCACAGAGATTCTTCTTCAAGAGATTTTTGCAAGTACTGGTCCTATTGAAAGCTGTAAACTCATCAGAAAGGAT

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
  | ||  |||| |   ||    |  |  |||||         |||| ||||||| ||  ||  |   |||| |||| |   |  ||||||| || |||||||| ||||| ||||| ||||  |||||  ||||||| || |||||||||||||||||  | ||||||||||| ||| |||| || ||  |||| || |||
gatgttgagggacttgtagccc-tgctaatttttatgtttttgtttcattgttctgtttcttgtttagatttttagtctgcctgcctttgagaaattgcagGTACGTTGGAAACATCCATATTCAGGTGACGGAACCTCTGCTTCAAGAGGTTTTTGCTGGCACTGGTCCTGTAGAAAGCTGTAAACTAATTAGGAAAGAA

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|161716028|gb|FC065534.1|FC065534
EST:     CCAAGTGGAAATCTGCCTCCTTGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATATCGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|349811318|gb|FQ407544.1|FQ407544
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|161721264|gb|FC069684.1|FC069684
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|110694202|gb|EE071104.1|EE071104
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATATCGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|351031018|gb|FQ439054.1|FQ439054
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|27755123|gb|CB035878.1|CB035878
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|77582239|gb|DV220083.1|DV220083
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATATCGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
EST: gi|110357183|gb|EC920553.1|EC920553
EST:     CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT                         GTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT
genomic: CCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgttt ... ggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA
                     aatttatagtttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttggggattcaaaggggattttcctttttgctcaagcttttctttgttcttttcttttctagaatttatagtttctttatctttgaggaaatgcagGTATGTTGGGAACATTCATACGCAGGTATCGGAACCACTTCTTCAAGAGGTTTTTGCAAGTACTGGTCCTGTTGAAGGCTGCAAGCTCGTTAGAAAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- ttttggg