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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaaatatctaatgaagacaatgtttttgagtccaaaaataataatttttaaagcctaatatgttgcctgccataaactaactctctcttcctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG

Basic information

species Vitis vinifera
transcript Vv13s0019g04170.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g48620.1 (Oryza sativa), 3'ss of exon 12
tacaaatatctaatgaagacaatgtttttgagtccaaaaataataatttttaaagcctaatatgttgcctgccataaactaactctctctt---cctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
  ||| ||||| ||  | ||  | |||    || |||| || || |||||    |  | |   ||  |   | |||     | | |||  |     ||||||||||||||||||| ||||| ||  ||||||||||||| || |||||||| || ||||||   || |||||||||||   | | ||||||||| | || |||
-gcaagtatctgatagatacttt-tttcactgttcaaacattatgatttt---ggttttaccagtc-ctcacaatactgatattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG

upper sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G35580.1 (Glycine max), 3'ss of exon 12
tacaaatatctaatgaagacaatgtttttgagtccaaaaataataattt--ttaaagcctaatatgttg--cctgccataaactaactctctcttcctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
   || |||  |||    | |||  |     ||  ||| | |  | | |   |      || |  | ||   |||   | ||||||||  || |  ||   ||| ||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| ||  |||| |||
---aagtattcaatatccagaattgtaacatgttaaaacaaagcactctaacttgcttttagttgggtgaatctgttgtgaactaacttgctttctcttt-cagCGAAAAGGATCAGGCTGAAAACCTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTTTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG

upper sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G31970.1 (Glycine max), 3'ss of exon 15
tacaaatatctaatgaagacaatgtttttgagtccaaaaataataattt--ttaaagcctaatatgttg--cctgccataaactaactctctcttcctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
   ||||||  |||    | |||  |   | ||   |  | |  | | |   |       | |  | ||   |||   | ||||||||  || |  ||   ||| ||||| ||||||||||||||  ||||||||||||| |||||||| ||||||||||| ||||||||||| ||||||||| ||||||| ||  |||| |||
---aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctcttt-cagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG

upper sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G28880.1 (Arabidopsis thaliana), 3'ss of exon 13
tacaaatatctaatgaagacaatgtttttgagtccaaaaataataatttttaaagcctaata-tgttgcct-gccataaactaactctctcttcctca--acagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
        |  |   || ||  |||| | || ||    |||  |  ||  |    |  |  | || | | |   | |    |   || |  |  || |  ||||||| ||  |||| || || ||||||||||||||||| |||||||| ||||| || |||||||||||||| ||||| ||  | ||||| |||   || |||
-------gtacaccaaacacgttgttctagaatcattgaatgtttcttaattgttcacatcaatgctactttaacgttgtttttttccccatgtcttataacagTGAGAAGAATCAAGCCGAGAATCTGATGATTGTTGACCTTCTAAGGAATGATCTCGGTCGTGTCTGTGAGCCTGGCTCAGTCCATGTACCTAACCTCATG

upper sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S149_275V6.1 (Physcomitrella patens), 3'ss of exon 12
--------------------------------tacaaatatctaatgaagacaatgtttttgagtccaaaaataataatttttaaagcctaatatgttgcctgcca-taaactaactc----tctcttcctcaa-------cagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
                                | |     ||| | || | | |  | ||   |  |  | |||      ||||            |||| ||  | |||||| | |     ||| ||  |          |||||| || ||    || || |||||||||||||| |||||||| || ||||||||||| || || |  ||||| || ||| | ||||| ||  | || |||
gtatgattactttggttgcatggtttccactttgctttgttctcacgaggcctaattctt---gctcgtagatagctggctttagtttacctgggcttgcttgttaataaacttattgaaggtctgtttttggtgtgattccagTGAGAAGGACTTTGCAGAGAATCTGATGATTGTAGATCTTCTGAGGAATGACCTTGGACGAGTTTCGGAACCAGGTTCTGTGCATGTGCCCAGCCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttaaagcctaatatgttgcctgccataaactaactctctcttcctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
                               aactaac  putative branch site (score: 1)
                                 ctaactctctcttcct  CT-rich tract
            taatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaaatatctaatgaagacaatgtttttgagtccaaaaataataatttttaaagcctaatatgttgcctgccataaactaactctctcttcctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG

-acaaata
- - - - - - - -aagacaa
- - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - taaagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa