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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcctatttattaatgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgattggtattttttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA

Basic information

species Vitis vinifera
transcript Vv01s0011g03350.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 5
tgtcctatttattaatgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgattg----gtatttt-------ttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA
             ||| |    | ||| | || | | || |  | ||| || |    ||||  |   || | ||||||| ||     || |||        | |  | ||||| |  |  ||||| || |  || || |  | || |||||||||||| ||||||||||| ||||| |||||||
---------agaaaatactagaactgatcctt-tctatgttagtagaa-tattccaatattagagatatacatgacctgtttactcagtgtttgaatattatgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGGGATGATGCCGAGGGGTACTATA

upper sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G42220.1 (Glycine max), 3'ss of exon 10
tgtcctatttattaa---tgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgattggtatttt-----ttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA
   ||| | | | ||   ||||||    |    | |||   ||||||     || |   ||||||       | || ||   |||   ||||      |||||||||||||| ||||||||| ||||| ||||| |||  ||| || |||||||||||||| ||||||||||| || ||||
---cctctctgtcaagcttgccttttagggtaatagtt---gatttttcgtttatttatttatttgctcttagattaact--attaagatttcctaccttcttttcagGGAAAAGGAGATGGTTTACTGATTGAGAGGGCTGGCCTACATGACAATTGGGACGATGCAGAGGGTTATTATA

upper sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G24820.1 (Glycine max), 3'ss of exon 7
tgtcctattta---ttaatgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgattggtattttttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA
||||    ||    |||  |   |  ||||  |||  ||   ||||    | | || ||||||  |    ||     |      |  | |   |||||||||||||| ||||||||| || || ||||| |||  ||| || |||||||||||||| ||||||||||| || ||||
tgtcaagcttgcctttagggtaataggtgatttttcgttc--atttatttatttat-tcttatgacttatattaactattaagattttctaccttcttttcagGGAAAAGGAGATGGTTTGCTGATTGAGAGGGTTGGCCTACATGACAATTGGGACGATGCAGAGGGTTATTATA

upper sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G20810.1 (Glycine max), 3'ss of exon 7
tgtcctatttattaatgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgat-tggtattttttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA
  |  |||    ||  |   | | |   || | | | |  ||| ||   | ||      |||   |  |   |  | | |  |    ||  ||||||  |||| | |||||| || ||||  ||||| ||| |||| ||||| ||||||||||||||||||||||| || || |
-tttttatgacatacagttgtcaatctactgtttatttagtttggggttttattgtaggtttgttttcttggtatcttaagatttccttccttctttgaagGGTAAAGGAGAAGGTTTACGGATTGAGAGGGGTGGCCTTCACGACAATTGGGATGATGCAGAGGGTTATTACA

upper sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G25840.2 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------tgtcctattta--ttaatgccttga-----gtga---cctttgtttgtgat-tttggaactaatatctta-----tttcaatcatgcttgacctg----attggtattttttcttttcagG--GAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA
                                                                      |||| | || |  ||| ||  ||||      |||   ||||| | | |  | ||||     ||| |  |      ||| |||  |   |   ||     |||        |||||||  ||  | | ||| |||||  | |  || |  ||||| || |||||||| |||||||||||||||||||| || ||||
gtatgtatttaacttaactacttcatatcgtctaaccgtgtatttgtactgtttactaaccttctgatgttgtcatcttaagtttactgttttgatcatcatgaaaccctttttctttagtgtttgaggaaaattttgtgagggtttttaatattttcttttctcttatattaaacccacttcttttagGGAGGGAAAGGTGATGGTGTTCCCATGGTGAGGAGCGGGCTTCATGATAATTGGGATGATGCAGAGGGTTATTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactaatatcttatttcaatcatgcttgacctgattggtattttttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA
                                       tattttttcttttc  CT-rich tract
     aatatcttatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcctatttattaatgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgattggtattttttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - taatgcc
- - - - - - - - - - - - - - - - - - - - - - - aactaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg