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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcagaccctaatctattttatgaacaaatgtggctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG

Basic information

species Vitis vinifera
transcript Vv11s0052g00880.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 15
----------------gtaagtcagaccctaa-tctattttatgaacaaatgt---------ggctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG
                  | ||  |    | | |   |||| |||| | |  |            |||| |||  |||   |    ||  ||| |||  |    || |||   |  |||||||||| |||||||| ||| |||||  ||| ||| |  ||||||| || || ||||| ||| |||| ||||| || || |||||||||||||| ||||
gtgagttatctatcctccatgtaggtttatgagttctttttctgaaaagagatttatgagttaattataatttaggtcggcttaccaatattattttaata-atttttat---taaagGACTACATCTATGAAGACGAGTTGAATCACTTCGTTAATACTGGTGCACTTTCTGAGCTCATTCTTGCCTTCTCTCGAGAGGGACCCACCAAGGAGTATG

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagtcagaccctaatctattttatgaacaaatgtggctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG
||||   || |  || || |   |     ||||  |  |  |  ||| |||| | |       | ||||  | | | ||  ||| |  | |||| | ||| || || || |||||  |  | ||||||||   |||||| ||| ||||||| | ||| || ||||| ||||||||||||||||| ||||| |
gtaataaagccattactcaaaact-----caaacctttcattggttt-tgtccagt------ttctaatcatatcttctcatatat--gtagGATTTCATCTACGAGGAAGAGCTCCAGCGATTTGTTGAGAGTGGTGCTCTCGCAGAGCTAAGTGTCGCCTTCTCTCGTGAAGGACCCACCAAAGAATACG
















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|32267884|gb|CD717043.1|CD717043
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|27582064|gb|CB004759.1|CB004759
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|32270252|gb|CD719411.1|CD719411
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|56409444|gb|CX017696.1|CX017696
EST:     GGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: GGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|30324587|gb|CD007849.1|CD007849
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|30326071|gb|CD009333.1|CD009333
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|352774216|gb|FQ474739.1|FQ474739
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|30300181|gb|CB976975.1|CB976975
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGATGAGCTGAATGGCTTTGGTGGATCTG
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTG
EST: gi|110699884|gb|EE077290.1|EE077290
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|30322494|gb|CD005756.1|CD005756
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
EST: gi|32271899|gb|CD721058.1|CD721058
EST:     CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATG                         GACTACATTTATGAAGACGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC
genomic: CAGAACTAGGATCATCCATATTATTCTTTGGATGCAGGAACCGAAAAATGgtaagtcaga ... atctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG
                         ctttaat  putative branch site (score: 4)
                                        cttctatcttt  putative PPT
                    tgaaactttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcagaccctaatctattttatgaacaaatgtggctatattttgtgtcaaatgtgaaactttaattttgtgtgcttctatctttgcagGACTACATTTATGAAGATGAGCTGAATGGCTTTGTTGAATCTGGTGCGCTCTCAGAGCTGATTGTTGCTTTCTCACGTGAAGGACCCACCAAGGAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA