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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

Basic information

species Vitis vinifera
transcript Vv09s0002g02470.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 8
------------------------------------tgcattgatcagggaaaaa---------gaaaaaaaaaatc----attttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgata----gtac---ttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                                      ||||| | ||    |||         |||  ||||| |     || ||  | || ||  ||| |||  |      || |         ||  | | |    || |   ||   ||||| |||||||| || ||||||||||| || ||||| ||||| |||||||||||||| ||  ||||||| || |||||| | | |||||||||    || || 
gttagtaacccccttgcacttcctaatggaacatttatcattgtttagaaggaaatgttcgatggaattaaaaagttgcaaatgtttgaagttaatttttatatggataaaatttgcacaagctgttctctaaaataaagtgcgcattctgtgcagATTTGAGGAGCATGAGGCACCTGGATCGAGATCCTTTTTTACAGAGATAATTGCATCGGTTTCAGATATAAAATTTGCAAGGGATGGAAGGCACATTCTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttat-ttagtgct----ctttcctggatcagtcagtgatagta----cttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                                                               || | |  |   |      |  |            |  ||| |   |  || |||  ||||  |      |  |   |||||   | ||||  |    | |  |  ||| ||||||||||| || |||||||| |||||||| || || ||||||||||| || ||||| || || || |||||||| | |||||||||||  || || 
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcat--aagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 8
------------------------------tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                              | || |  |||    |    |     |  | ||| | |  | |   | | | |  || || || |||  |     ||  | |  || |   ||  || || |||||| | || ||||| || |||||||||||||| || || ||||| || ||||| ||||||||||| || |||||||||||||| |||  ||| |||
gtgagttttcatttgttactcatactctttttcaatattcaacatagtttatttggatgagcatctggtggattggcctgtcttgttcgtactattttttattatagctattcctattctatgtgtgtagCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTCTTTACTGAGATTATAGCCTCGATTTCAGACATAAAGTTTTCCAAGGATGGGAGACATATTCTC

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 8
--------------tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgttt---ttatttagtgctctttcctggatcagtc--agtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                || | |          |     | || ||||  |  |   |   | | |   ||||    |    ||   || |  | |   |    |  |   | | || || |||||| | || ||||| || |||||||||||||||||||| ||||| || || |||||||| ||||| |||||||| |||||||| ||   ||| |||
gtgagcttttatttcacactaacatatactctacttggagaatatcaagtgaatactgcccttctcaattatcctataagtttcgttgtactatttctatacctgttgtcttcttgtagCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTC

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
--------------------------------tgcattgatcagggaaaaagaaaaaaaaa--atcattttgaagg----taaacgtttt-----tatttagtgctctt--tcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                                    ||||| ||     ||     | |    |||||||  || |     |||| ||||     |||||| || || |  || |   |   | |      | |  |   | ||| |||||||| || || |||||||| |||||||| ||||| ||||||||||| || ||| ||||||| || |||||| | | ||||||||||   || || 
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatct-tgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 8
---------------------------------------tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                                       | || |   |           || |     |   |    |  | | |  || |  | |  | |   |  |   |   |   || |  |   | | || || |||||| | || ||||| || || ||||||||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||| ||   | | |||
gtgagcttttagtttacactttttatttcctacaatatgttcagtatactctacttggagaatattgggtggatactgaccttatcaattatcctaaaagtttccttgtatttttatacctgttcatgtcttcttgtagCTTTGAGCAGCATGAGGCCCCAGGCTCAAGATCATTTTTCACTGAGATTATAGCCTCAATTTCGGACATAAAGTTTTCGAAGGATGGGAGGCATCTTCTC

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
-tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttag--tgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
        |  | ||    ||   |   | | ||| | |    |||    | ||    |   |  | | |  |  || ||| |   |  |  | |  |  ||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| |||||||| || || || ||||| | | |||| | || ||| || 
cctagacaactaaggctgtagcctatgtataacatat-gctaataatttatattgcagaagttattatatgttttatgagttaacaaagg--cctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttattta-----gtgctctttcctggatcag--tcagtgatagta--cttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
             | | |  || ||||  ||  || || |    |   | |||||| |     ||| | | |  ||    ||  |||  || | |    ||   | ||| |||||||||||||| || ||||| ||| ||||||||||||||||||| ||||||||||| |||||||| ||||||   ||||||||||||| |||||| 
---------ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
-tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtga-tagtac-ttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
 |||||  |  ||| |||            | | | ||  |  |  |    ||||| |  |  | |||   ||   | |||  || || ||| ||   | ||| |||||||||||||| || ||||| || |||||||||||||||||||| || || ||||| |||||||| ||||||   ||||||||||||| |||||| 
ttgcat--acaaggaaaaccatttttctggagcctattatatatgtattcatttatgtgat-ttgttttgcggtaaactcacagaatattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 8
tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagt-gctctttcctggatc--agtcagtgatagtacttgcat-----gcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
        | | | | ||        ||     || |     | ||  | | |||||  |   |   |  | ||    | | |   |||    | ||||     |||| ||||||||||| || || || || || |||||||||||||||||||| ||||| || || |||||||| ||||||   |||||||||||||  ||||| 
--------tgaagcagaatttttctgaagcctgttatatgcatgaatttatgtatttttttaatagctggtagactctaataaacaatacccttggcatttgatgcagATTTGAGGAACAGGAAGCCCCAGGGTCCAGATCATTTTTCACAGAGATTATTGCTTCTATCTCAGACATAAAATTTGGGAAGGATGGAAGATACATACTA

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 8
-----tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
      | |||  || |  ||       | |   || | |||     |     ||  ||  | ||   || |  |  |  |  |  |  | | | ||| |||||| ||||||||||| || || || || || |||||||||||||| ||||| ||||| || || || ||||| ||||||   |||||||| ||||  ||||| 
gaagcagaatttttctg--aagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaacaataccct--tggcatttg-atgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT

upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------------tgcatt---gatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttat-ttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
                                                                                     | ||||    ||                 | ||     ||| |  | ||  ||  ||   ||  | |  |  |   |     || || |  | | |     ||| ||||| ||||  || |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||| ||||  ||||| 
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgacc--actgaccattgttgcttcatat-cacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
     tttatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
tgcattg
- - - - - - - - aaagaaa
- - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - -aggtaaa