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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgttgcaattatgcttctataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT

Basic information

species Vitis vinifera
transcript Vv08s0058g00890.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 11
gttttgttgcaattatgcttctataactcttcaattaccctctatttgctaaatttcctacaacc---gtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
       ||   || |   |  | |||| |  |||  |   |  ||   |  |||||  |  |     ||  ||| | ||   |     || |   || | ||||||| ||||||||  |||| || ||||| || ||   ||| || |||||||||||||||||| |||| || || || || ||||||||||||||||| |
------gtggtgttctatgttgaaaact-tgaaatctctgacagttcattttatttctcaagattcaggtatttacttagttgctctgtttttcaaatgacagTCATGCCAGGTTGACTTGGTGAAAGATGGAGGGCATGCATACTTTATCAGGTTTCTTGACAGTTTGGATGCTTACCCAGAGCAGCGTGCAATGGCTGCTT

upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 12
--gttttgttgcaattatgcttctataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
    | |  |    | |    |  | | ||||   | | |  | |||||   ||  |||    |          |||      || | ||     || | ||||||| ||||||||  |||| || ||||| || ||   ||| || |||||||||||||||||| |||| || || || || ||||||||||||||||| |
gtagtgttctatgttgaaaacttgaaatctctgacagttcattttatttctcaagattcaggtatttac-----ttagttgatctgtttttca-aatgacagTCATGCCAGGTTGACTTGGTGAAAGATGGAGGGCATGCATACTTTATCAGGTTTCTTGACAGTTTGGATGCTTACCCAGAGCAGCGTGCAATGGCTGCTT

upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 12
gttttgttgcaattatgcttc--tataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
        | |   |  ||||  | |||   || ||     || |  |||       || || |  |     | | | |  |  | | || |   || | |||| || ||||||||| |||| || ||||| || |||| ||||||  | ||||||||||||||| |||| || || || |||||||||||||||||||| |
--------gtatgcactcttcattgtaatattttaagagttcttttattg-------tcttagattcaggtgtttaacgtttagttttttctcaaatgacagTCGTGCCAGGTTGATTTGGTTAAAGATGGAGGACACACATATTTTGTTAGGTTTCTTGACAGTTTGGATGCTTACCCAGAACAGCGTGCAATGGCTGCTT

upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 3
gttttgttgcaattatgcttc--tataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
        | |   |  ||||  | |||   |  ||   |  | | ||   |   |    || |  |     | |||    |   || ||     ||   |||| |||||||||||  |||| || ||||| || || | |||||| || ||||||||||||||| |||| || |  || ||||||||||||||||| || |
--------gtatgcactcttcattgtaatcttgtaaggtcattttgttgtttctttagattagattctgttgttttacctgtaacattttcccaaatggcagTCTTGTCAGGTTGACTTGGTTAAAGATGGAGGACATACATATTTTATTAGGTTTCTTGACAGTTTGGATGCTTTCCCAGAACAGCGTGCAATGGCCGCTT

upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 12
gttttgttgcaattatgcttctataactcttcaatt----accctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
 |         |||||  |    |||   || |  |    || ||  || |      | | ||    | | || |  | |   |||  |  ||   | |  |||||||||||||||||||| || ||||||||||| || || ||||| || | ||||||||||||  ||||||||||||| || || || ||||||||||| |
-tacgacctttattattttctactaaaatttgatcttgaaactctgcatgttgcgtgtctactgtgtcggacaatgatgatgttccatttctg---ggttgtagTCATGTCAGGTTGATCTAGTGAAGGATGGTGGTCATATCTATTTTATTAAGTTTCTTGACAGCATGGAAGCATATCCAGAGCAACGCGCAATGGCTGCTT

upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 12
gttttgttgcaattatg--cttctataactcttcaattaccctctatttgctaaatttc--ctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
 | |       |||||   || ||| || |      | |  |||||  || |  || ||  ||    | | || |  | |   |||  |  ||   | | ||||||||||||||||||||| || |||||||| || || || ||||| || | ||||||||| ||  ||||||||||||| || || |||||||||||||| |
-tatgacctttattattttctactaaaatttggtcttgaaactctacatgttgcatgtctactgtgtctggcaatgatgatgttccatttctg---ggttatagTCATGTCAGGTTGATCTAGTGAAGGATGGCGGTCATATCTATTTTATTAAGTTTCTTGATAGCATGGAAGCATATCCAGAGCAACGTGCAATGGCTGCTT

upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ28980 (Selaginella moellendorffii), 3'ss of exon 12
gttttgttgcaattatgcttctataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
                                          || | ||  | |      ||   |     ||   |  || |    ||| |   |   ||| ||||| ||||||||||| || |||||||| |||| |||||| ||||| || || ||||||   || |  ||  ||||||| |  |||||||| || |
-----------------------------------------gtaatggc--attactgagcagtagattgcatcctgcttcttgaactgttttgca---gTCCTGTCAAGTTGATCTGGTTAAAGATGGTGGGCACAAATATTTTATCAGATTCCTGGACAGTCCAGACGTGTACGCTGAACAACAGGCAATGGCAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT
 tgctaaa  putative branch site (score: 2)
                     tcattattaagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgttgcaattatgcttctataactcttcaattaccctctatttgctaaatttcctacaaccgtcattattaagaatcctatcttgtgtgataatagTCATGTCAGGTTGATCTGGTAAAGGATGGTGGCCACATATATTTCATCAGGTTTCTTGACAGTGTGGAAGCATATCCTGAACAGCGTGCAATGGCTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - tgttgca
- - - - - - - -tgcttct
- - - - - - - - - - - - - ctcttca
- - - - - - - - - - - - - - - - - - -ccctcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cctacaa