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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtaattactggtagaatgtacgagaaaattgcagtttgcttctgatgaagttattctattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC

Basic information

species Vitis vinifera
transcript Vv03s0091g00080.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G40730.1 (Glycine max), 3'ss of exon 2
gagtaattactggtagaatgt-acgagaaaattgcagtttgcttctgatgaagttattc-tattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC
|  | | |  | ||    | |   ||  | | || ||||   | |  ||  | |||||  |  ||  |  |||| ||    |||| |||| ||||  ||||||||| ||||||||||| ||||||||||||||  ||||||||||||| ||||| ||||| || || || ||||| ||||| || ||||| |||||||| ||
ggttgaatgatagtctcttcttgtgactataatgaagttc-ttacaaatttaattatttatggtgttaccattggattgaattcatattg-gcttcttgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAGCAGGTTGTTTTCTCCGACCCTTATAAAGTTTCTCAATATAATCGTTGGACTTCCCC

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G26580.1 (Glycine max), 3'ss of exon 2
-gagtaattactggtagaatgtacgagaaaatt-----gcagtttgct-tctgatgaagttattctattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC
    || |  || || |    ||  || || ||      || ||   | |||  ||  ||||   |        ||||||||    |||| |||| |||| |||||||||| ||||||||||| ||||||||||||||  |||||||||| || || || |||||||| || || ||||| ||||| || ||||| || ||||| ||
ctgatattctcttgttgtgactataaggaagttcttacacatttaattgtctattggggttaccttg------ggattgaattgaattcatattg-gcttcatgcagTTGCCGAATTTTGTGGGAATGTGGAGTTATGCAGGCTCACTGAACAGGTCGTTTTCTCTGACCCTTATAAAGTTTCTCAATATAATCGTTGTACTTCCCC

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 2
gagtaattactggtagaatgtacgagaaaattgcagtt-tgcttctgatgaagttattctattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC
                   || | | |   |  ||  | |  |  | |  |    ||  ||| |    | ||| |    ||     ||||| ||| || |||  | |||||||||||||||||||||||||| ||  | || |||||||||||||| || || ||||| | ||| ||    |  ||||| |||||||| ||
-------------------gttcaaaaccctcacatctattttatttactagtcaatgttatcgtgttgcttgtagtgagtgtcttttgtg-tttgtgtagTAACCGAATTTTGTGGTAATGTGGAGTTATGCCGATTAACGGAGCAAGTTGTGTTTTCGGACCCATATAGAGTTTCCACATTTAATCGTTGGACTTCACC

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|161714716|gb|FC064488.1|FC064488
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|30324984|gb|CD008246.1|CD008246
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|161720482|gb|FC070594.1|FC070594
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|71863664|gb|DT012719.1|DT012719
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|161712718|gb|FC062290.1|FC062290
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|32248279|gb|CD714098.1|CD714098
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|110727535|gb|EE104406.1|EE104406
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|32269752|gb|CD718911.1|CD718911
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|37184887|gb|CF604240.1|CF604240
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|30326383|gb|CD009645.1|CD009645
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|32247178|gb|CD712997.1|CD712997
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
EST: gi|46917661|gb|CN546990.1|CN546990
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTG
EST: gi|110727897|gb|EE105184.1|EE105184
EST:     TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAG                         TTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG
genomic: TTTCTTCACATCTCTTCTATACCATGACACAACCGAGCACAAACGTGCAGgtaaatgctt ... ctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgaagttattctattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC
             tattgac  putative branch site (score: 2)
       ttattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtaattactggtagaatgtacgagaaaattgcagtttgcttctgatgaagttattctattgacaagattgaatcatgttcaaattgtgctttatgcagTTGCTGAATTTTGTGGTAATGTGGAGTTATGTCGGCTCACTGAGCAAGTTGTGTTCTCTGATCCATACAAAGTATCTCAGTACAATCGGTGGACTTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - ttactgg
- - - - - - - - - - - - agaaaat
- - - - - - - - - - - - - - - -tgcagtt
- - - - - - - - - - - - - - - - - - - tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttc