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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtttattatctttttttgtagtggtgttaaagtaattcatatctaaatacaggagctgacttgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA

Basic information

species Vitis vinifera
transcript Vv00s1206g00020.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G40060.1 (Glycine max), 3'ss of exon 7
-------------------------gttgtttattatctttttttgtagtggtgttaaagtaattcatat----ctaaatacaggagctgac-----ttgagctaaaattttg---------------tccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA
                          |  |||||| ||| ||||| |   ||   |  ||| ||||| ||     ||   ||    ||| ||     |  || |   ||  ||               |||||||||||   |||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| |||||||| |||||  | ||||| 
gtcttgcttctttgctctcctatttttcttttattttctctttttatttaggatctttagtgattcacatggtgttagcaactactgcttacaactctcaaggtggcatactgacaattaattgatattccagTGGGGCTGTTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCATGGCCC

upper sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G00740.3 (Glycine max), 3'ss of exon 7
------------------------------------------gttgtttattatctttt----tttgtagtggtgtta--aagtaattcatatctaaatacagg-agctgacttg-agctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA
                                           || ||||  ||||||     ||  || ||||||||  || || | | ||   |  |  |||  ||  |||   |  |||    |  |||||||| ||   |||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| |||||||| |||||  | ||||| 
gtcttgcttctttgctctcctatttttctgttattttctctatttatttaggatctttagcaattcata-tggtgttagcaactactgcttacacatctcaaggtggcatactaacaattaattgatattccagTGGAGCTGTTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAAAGATTTCAGCTTTCCAAGCATTTCTCCTTCTCCTGGCCC

upper sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G12980.2 (Glycine max), 3'ss of exon 7
------------------------------gttgtttattatctttttttgtagtggtgttaaagtaattcatat---------ctaaatacaggagctgact--tgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA
                               |  || ||| | ||  |||| |  | ||||  || |||   | |           |||||  |   || |||  |||   | || | | || ||||| ||   |||||||||||||||||| ||||||| ||||||||| ||||| || |||||||||||||| ||||| |||||||| | |||||||||||||
gtccttcttcttttctttcttattatccttttccttgatttttttggtttgcaa-gttgtttgagcaatcactgtgctcaaccctcaaatagggcttcttactaatgattgataaatctatc-agTGGAGCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCA

upper sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G12970.1 (Glycine max), 3'ss of exon 4
--gttgtttattatctttttttgtagtggtgttaaagtaattcatat---------ctaaatacaggagctgact--tgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA-----
   |  || ||| | ||  |||| |  | ||||  || |||   | |           |||||  |   || |||  |||   | || | | || | ||| ||   |||||||||||||||||| ||||||| ||||||||| || || || |||||||||||||| ||||| |||||||| | |||||||||||||     
ttttccttgatttttttggtttgcaa-gttgtttgagcaatcactgtgctcaaccctcaaataaggattcttactaatgattgataaatctatc-aatggagCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGATTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAAAAAA

upper sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G02070.1 (Glycine max), 3'ss of exon 7
-------------------------------------gttgtttattatcttt----ttttgtagtggtgttaa-agtaatt---cata-tctaaatacaggagctgacttgagctaaaattttgtc---cagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA
                                      || ||| ||||   |    | |||   || |||||  | | | |   || |  |   | | |||   ||     | ||     ||  ||   |||||| ||   |||||||||||||||||| ||||||| ||||||||| ||||| || || ||||||||||| ||||| |||||||| | |||||||||||||
gtattttttctcttctttcttattatccttttcctagatttttttttattcctaaattgttgatatgatgttagcaatcactgtgcacaaccctcaaatagggcttgttactaactgttgattaatcaatcagTGGAGCTGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATTGAGAGATTTCAGCTTTCAAAGCATTTCTGCTTTCCTTGGCCA

upper sequence: Vv00s1206g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G12970.1 (Glycine max), 3'ss of exon 3
gttgtttattatctttttttgtagtggtgttaaagtaattcatatctaaatacaggagctgacttgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA------
                                                                                     || |    |||||||||||||||||  ||||||| ||||||||| ||||| ||  |||| |||||||| ||||  || || ||||||||||||||||||      
-------------------------------------------------------------------------------------ggagttgttcatttcatggcttcaagcaatgactctggagttagagacttggatgtggaaagatttcaacttttgaaccacttttcctttccttggccagTGAAT

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|33409772|gb|CF215399.1|CF215399
EST:     TATGACGACAATGCTATCACAAATGCAGTAGAGATTTATGATAGTCCCAG                         TGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTT
genomic: TATGACGACAATGCTATCACAAATGCAGTAGAGATTTATGATAGTCCCAGgttgtttatt ... ttttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTT
EST: gi|349827954|gb|FQ422822.1|FQ422822
EST:     CAAATGCAGTAGAGATTTATGATAGTCCCAG                         TGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTT
genomic: CAAATGCAGTAGAGATTTATGATAGTCCCAGgttgtttatt ... ttttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTT
EST: gi|294964449|gb|GW838252.1|GW838252
EST:     TATGACGACAATGCTATCACAAATGCAGTAGAGATTTATGATAGTCCCAG                         TGGGGCCACTCATTTCATGGCTTCAAATAATGACTATGGAGTTAGGGACTT
genomic: TATGACGACAATGCTATCACAAATGCAGTAGAGATTTATGATAGTCCCAGgttgtttatt ... ttttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaagtaattcatatctaaatacaggagctgacttgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA
                                     agctaaa  putative branch site (score: 3)
                                             ttttgtcc  CT-rich tract
      taattcatatctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtttattatctttttttgtagtggtgttaaagtaattcatatctaaatacaggagctgacttgagctaaaattttgtccagTGGGGCCACTCATTTCATGGCTTCAAATAATGACTGTGGAGTTAGGGACTTCGACATGGAGAGATTTCATCTTTCTAAGCATTTTTCCTTTCCTTGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA