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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaaaacactgaattaaacatgattcactattttatagttctttgctttcctgctgaatctgctgctgtgttttattttgtggttacaatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC

Basic information

species Vitis vinifera
transcript Vv12s0055g00460.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g36190.1 (Oryza sativa), 3'ss of exon 3
---ttttaaaacactga-atta-aacatgattcactattttatagttctttgctttcctgctgaatctgctgctgtgttttattttgtggttacaatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC
   | |  ||| | |    |||    ||| || |  |  |   |  |  ||| ||||   ||||||    |    ||  | | |   || ||    ||  | ||||| | || |  || | ||| ||||||||  | || || |||||| | |||   ||||| |||||||| ||||||||||| |||||||| || ||||||||
ttttctccaaatatttttgttatggaatgtttaaacaactggcaaat--ttgatttcac-ctgaattgaataagttggctcactac-tgatttttgttaat-cagCTGTACTTGCGGATAGTGGCAAGTTCCTCTTGTCCGCTAAAAGGCACCGCAAAACAACCTGCACAGAATATGTTATCTCAATGGATGCAGACAACATTTC

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G19520.4 (Glycine max), 3'ss of exon 5
ttttaaaacactgaattaaacatgattcactattttatagttctttgctttcctgctgaatctgctgctgtgttttattttgtggttac---aatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC
   | || ||  || |   | ||      | || || |||| | |      |    | ||| | ||  |   |||  ||||    ||||    | ||||||||||||| ||||||||||||| || ||||| |||||||| || ||||   |  | ||||||| ||||||||| ||||| |||||||||||||| ||||| ||
-actcaatca--gagtctgatatttactgccatattctagtgcatacagagctcatttaattttcttttccatttattttttaatttactttgagttttgcagCTTTGTTAGTTGAAAATGGAAAATTCCTCCTTTCTGCTAAGAGGACAAGGAGAACAACTTACACAGAGTACGTTATTTCCATGGATGCTGACAACATCTC

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G05490.1 (Glycine max), 3'ss of exon 4
ttttaaaacactgaatta----aacatgattcactattttatagttctttgctttcctgctgaatctgctgctgtgttttattttgtggttac---aatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC
         ||| ||| |     | ||   |  | || || |||| | |    | |    | ||| | ||  |   ||| ||||| |  ||||    | ||||||||||||| ||||||||||||| || ||||| |||||||| || ||||   |  | ||||||| ||| ||||| ||||| |||||||||||||| ||||| ||
------gggactcaatcatagtgatatttattgccatattctagtgcatacagtgctcatttaattttcttttccattt-attttttaattactttgagttttgcagCTTTGTTAGTTGAAAATGGAAAATTCCTCCTTTCTGCTAAGAGGACAAGGAGAACAACTTACACTGAGTACGTTATTTCCATGGATGCTGACAACATCTC

upper sequence: Vv12s0055g00460.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G76900.1 (Arabidopsis thaliana), 3'ss of exon 3
ttttaaaacactgaattaaacatgattcactattttatagttctttgctttcctgctgaatctgctgctgtgttttattttgtggttacaatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC
               | |||| | |||  || | || | ||||   | ||| ||      ||    ||        || |    |    ||| |||||||||||| | ||||| ||||| ||||| ||||||||||||||| | |   |  | || || | ||| ||||| || ||||| ||| | || || | ||||||
--------------gtaaaacttcattttctctgtttttgttccaagtttttctctgttctccaaagcaa------atctgaaagcatgaatatttgcagCTTTGTTGGTTGAGAATGGAAAGTTTCTTCTTTCTGCAAAACGCATAAGAAGAACTACATACACCGAGTACGTGATCTCTATGCACGCCGACACCATTTC

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|161719261|gb|FC064814.1|FC064814
EST:     AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG                         CTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
genomic: AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTGgtaatcttct ... atttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
EST: gi|71863069|gb|DT012124.1|DT012124
EST:     AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG                         CTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
genomic: AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTGgtaatcttct ... atttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
EST: gi|71859885|gb|DT008940.1|DT008940
EST:     AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG                         CTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
genomic: AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTGgtaatcttct ... atttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
EST: gi|71890453|gb|DT039508.1|DT039508
EST:     AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG                         CTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
genomic: AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTGgtaatcttct ... atttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCC
EST: gi|71864896|gb|DT013951.1|DT013951
EST:     AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTG                         CTTTGCTAGTTGAAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGC
genomic: AAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTGgtaatcttct ... atttttgcagCTTTGCTAGTTGAAAA-TGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttcctgctgaatctgctgctgtgttttattttgtggttacaatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC
                                              tttttgc  CT-rich tract
                         tgttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaaaacactgaattaaacatgattcactattttatagttctttgctttcctgctgaatctgctgctgtgttttattttgtggttacaatttttgcagCTTTGCTAGTTGAAAATGGGAAGTTCCTTCTTTCTGCAAAAAGGAATCGCCGGACAACTTGCACAGAGTATGTTATCTCCATGGATGCTGAGAACATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - aaaacac
- - - - - - -aattaaa
- - - - - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtggt