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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatattatctactgcgctctgatttgaatgctgagccttttagatttccagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g04980.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 8
gtgatattatctactgcgctctgatttgaatgctgagccttttagatttccagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
   |||    |||         ||| |  ||   |    |    | | |  || |  |    | ||   ||  |   ||||    | ||| | ||||  |  |||||||| ||| | ||||||||||| || ||||||||  ||||||| || ||||| || || || || ||||||||||| ||| |||| || ||||||
--tataaatactaggatttagggatcttcatatagtttatacatggtatttagat-ttcatttgtaaccctattgaagacatcctgattgttgtctt--atgtagAGTCGACATCTTGAAGTTCAGTTGCTTTGTGATCAATATGGCAACGTAGCAGCACTTCACAGTCGAGATTGCAGTGTACAACGGCGACACCAAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 6
gtgatattatctactgcgctctgatttgaatgctgagccttttagatt----tccagttgctggagtt-tacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
      || | |||  |  | |  ||||||    ||  | |  | |||    ||   |  ||| |||| ||| |  |||| |     ||   |    ||||  |   |||||||| ||| | ||||||||||| || ||||||||  |||||||||| ||||| || || || |||||||||||||| ||| |||| || || |||
------ttctttacacc--tttattttgaagatggaagcctgaaaattgtgctctgttatctgtagttgtacattatattttatt--ttaaatcttattctctattgtagAGTCGGCATCTTGAAGTTCAGTTGCTTTGTGATCAATATGGCAATGTAGCAGCACTTCACAGTCGTGATTGCAGTGTACAACGGCGACACCAGAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 6
gtgatattatctactgcgctctgatttgaatgctgagccttttag-atttccagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
     ||  | |||  |  | |  |||  |||   |||||   |   |   | |||    |   | |    ||||  |     ||   |    ||||  |   |||||||| ||| | ||||||||||| || ||||||||  |||| ||||| ||||| || || || |||||||||||||| ||| |||| || || |||
-----atactttacacctttattttttagatgg-aagcctggaattgtgctctgttatctgtagtcatgcattatatttgatcttaaatcttattctctattgtagAGTCGGCATCTTGAAGTTCAGTTGCTTTGTGATCAATATGGTAATGTAGCAGCACTTCACAGTCGTGATTGCAGTGTGCAACGGCGACACCAGAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G377341_T02 (Zea mays), 3'ss of exon 4
------------------------------gtgatattatctactgcgc-tctgatttgaatgctgagccttttag-atttccagtt-gctggagtttacttcttattctgaca--attcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
                              ||  |  | ||  ||  |   |||| |  |    ||  | || ||  ||   |  || | || | | ||  | |  | |||| |  |||| ||  |||  |||    ||||| || ||| | || ||||| || || |||||| | ||||||||||| ||||| ||||| || || |||||||||||||||||  | || ||||||
gtgagaactgattcaaagattgtttcccttgttttcatgtcggctttgagcctgactctacctttgttctttgtatcatgagcgcttcggtgtaatatatatttgttcctgaaagcattcattctgttctttctttgtagAGCCGACATCTGGAGGTTCAATTGCTCTGTGATAAACATGGCAATGTGGCAGCACTGCACAGTCGAGATTGCAGTGTTCAAAGAAGACACCAAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 4
gtgatattatctactgcgctctgatttgaatgctgagccttttagatttccagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
|| | || ||| ||||  || |||| ||||||   | | |             ||  ||||||     || ||||||||  ||   ||| ||||||   || ||||| || ||| ||||||| |||||||| ||||||||| | || ||||| |||||  ||||||||||||||||||||||||||||| | || ||||||
gttagataatccactgatctatgatctgaatg---aacat-----------gattcttggagtcatggtcgtattctgattatctattttgtttct---aagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGAAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTGTTCAAAGGAGGCACCAAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 4
gtgatattatctactgcgctctgatttgaatgctgagccttttagatttccagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
|| | || ||| ||||  || |||| ||||||   | | |             ||  ||||||     || ||||||||  ||   ||| ||||||   || ||||| || ||| ||||||| |||||||| ||||||||| | || ||||| |||||  |||||||||||||||||||| |||||||| | || ||||||
gttagataatccactgatctttgatctgaatg---aactt-----------gattcttggagtcatggtcgtattctgattatctcttttgtttct---aagtagAGCCGACATCTAGAAGTCCAGTTACTTTGTGATCAGTACGGTAATGTCGCAGCTTTGCATAGCCGTGATTGCAGTATTCAAAGGAGGCACCAAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------gtgatattatct--actgcgctctgatttgaatgctgagccttttagatttccagttgc--tggagtttacttcttattctgacaattcgtttggtttcttc--aaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
                        ||||   | ||   ||| | ||| || ||  | ||   | |     ||||  ||| |   || | |    |||||    |  || ||  | |  ||| ||       |||||||| ||| |||| || ||| | || |||||  ||||||| |||||| |||| ||||||||||||||||| || || || ||  | |||||||||
gtatggctgcttaactatatctcttgatcgaagcttagctgagttcttatctggttactttac-tagagaatttaaagtagtaatgcattgcttttctttacatttcattttttctaattttttttttgtatagAGTCGGCATCTAGAGGTCCAGCTGCTCTGTGACAAGCATGGAAATGTTTCAGCTCTGCATAGCCGTGATTGTAGCGTCCAGAGAAGACATCAAAAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S13_171V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgatattatctactgcgctctgatttgaatgctgagcctttt-agatt--tccagttgctggagtttacttcttattctgacaattcgt--ttggtttcttca------aact--agAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
    |||| | |    ||   |  ||||  || | | | ||   |||||  |    ||| | | |  | |  |  |   | |||| |     |  |    ||||      || |  |||| || ||| | || |||||  | || ||||| ||   ||| ||||| |||||||||||||||||||| || ||||| ||||| || || ||||||
---gtattgtatgg-acgtggtcttttgcttgatcatcgttaggagattagttagattgtttgggact-ccccaaacgatcacaacttacaatctgccctttcatggtggaattgcagAGCCGACATCTCGAGGTTCAACTGCTTTGTGACCAATTTGGGAATGTGGCAGCCCTGCATAGCCGTGACTGTAGTGTGCAAAGACGGCACCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttgctggagtttacttcttattctgacaattcgtttggtttcttcaaactagAGTCGCCATTTAGAAGTTCAGTTACTATGTGATCAGCATGGCAATGTTGCAGCCCTGCATAGCCGTGATTGCAGTGTTCAAAGGCGTCATCAAAAG
                       ttctgac  putative branch site (score: 2)
                                         tttcttc  putative PPT
                 ttcttatt  TA-rich tract