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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

Basic information

species Vitis vinifera
transcript Vv11s0016g04180.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 13
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatattt-cagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
|   ||  |       ||   || | ||||      |    | ||    |||  | ||  | | |   |  |    | ||   |||||  ||||||| |||||||| |||||||||||||||||| |||||||||||||  | ||||| ||||| || |||||||||
gtgagtaattttgttcctggattta-aatttttttttgcgtgtcatttggaatattatgatgc-taaataggatctgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 4
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatattt-cagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
|   ||  |        |   |||| | |||    |  |  | ||    |||  | ||  | | |   |  |    | ||   |||||  ||||||| |||||||| |||||||||||||||||| |||||||||||||  | ||||| ||||| || |||||||||
gtgagtaattttgttcatggattcaaatttattttgcgt--gtcatttggaatattatgatgc-taaataggatccgctttcttatttgtagAATCTCTATTGGGCCGATAGTGGTGATTTAGTGACAATTGCAAGTGACACCTCATTCTACATTTTGAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttc-agAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
   ||     || |   |   || | | |||     |  |      |  |||  | ||| |  | |   | |  | ||  |  |||||  |||| ||||||||||||||||| |||||  |||| ||||| ||||||||| ||||||| |||||  | |||||||| 
--gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
   ||   ||||||   ||| ||  |  |     |   ||    |   |  |  | |   || |  | ||  | |  |       ||  ||||| |||| |||||||||||||||||  |||| ||||| ||||||||| ||||||| |||||| | |||||||||
--gtgag-tcaaaagtattatttttccttgggtggaaattttgtatgtatgagtttaatattaacctttt--gtttatcatgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 13
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaacta------atagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
    ||  |  ||    |||| | |  ||| | |   |||    |||   |  | |      ||  |      ||         ||   |  |  |||||||||| |||||||| ||||||||||||||  |||||||||||||| | ||||| ||||| || || || |||
----gtaatggaatttgttaccttattatttcaaacctttttttacattcatgccatttgaaatgttgtgccactcaaaacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 13
-------------------------gcatgttctcaaa---aagcttac-ttcacaattaccaggttttggccacagagaaactaatagtt-catttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
                           ||  | |||||       || | ||  ||||    ||||  ||||    || |    ||  |||      ||   |     ||   |  |  |||||||||| |||||||| ||||||||||||||  |||||||||||||| | ||||| ||||| || || || |||
gtaatgacatttgacatttgttgccttataatttcaaacctggttttgcatttccaatgtgaaggtaatggcatttgacatttgaaatgttgtgccactgaagacatgtttctttgtgtagAATCTTTACTGGGCTGACAGTGGTGATTTAGTAACAATTGCAAGTGATACGTCATTCTACATTTTGAAATATAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatt-----tctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
   ||     |  |   ||  |||     |   |  |||||   |   | ||  ||  |||| | |      ||||   |  |       ||  ||||  |||| |||||||||||||||||  |||| ||||| ||||||||| ||||||| |||||| | |||||||||
--gtgaatcaagtattattttttcttgggtgg-aaattttg--tatgtaaaatgtatgagtttactattaaccttttctttatcatgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 14
------------gcatgttctcaaaaagcttacttcacaattac-----caggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
               || |     || |  |||    ||  |       |   |||| |||  |  |  |||   | || ||| || |   ||       | |   ||||| | ||||||||||| ||||||||||| ||| |||| ||||| ||||| ||||| ||||| || |||||||||
gtgagtcgttacttttgcttcagcaatggatacccatcatgtgtttttactcttttttgccttaacgccactgg-aattgattactct---tgtgcctggtgt---agAATGTATATTGGGCTGACAGTGGTGATTTGGTGACAATAGCAAGCGATTCGTCATTCTACATTTTGAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gcatgttctcaaaaagcttacttcaca-attaccaggttttggccac-agagaaactaatagttcatttctttgggtgg--tttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
           ||  |||| | | |      | ||| |||  ||    |      || |  |||  ||  ||| | |    |||   | | |||||| || || ||||||||||| |||||||||||| | ||||| |||||| ||||||| || ||| | |||||||||
---------gtaagtgcttgcatgaggtggcatcagctttctgcttttatttcttcttactgtttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gcatgttctca-aaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
| | || ||   |  || | || |||   || |    |||    |          |  | ||| ||||  ||      |||   | | |||||| || || |||||||||||||||||| ||||| | ||||| |||||| ||||||| || ||| | |||||||||
gtaagtgcttgcatgaggtgacatca-gctttctgcttttatttcttcttactgtttcttgttaattttgttaaa--attttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
------------------------------------------gcatgttctcaaaaagcttacttcaca----attaccaggt---tttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
                                           ||  || |   ||  ||  | | |||    |||  ||| |     | | | ||   |   |  |   | | |  ||       |   ||  || |||||||||||||||||||| |||||||||||||| || ||||| |||||| | ||||| |||||||| |||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttgtcccaattagtgtctttactaactctttactcccatgaaaaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
------------------------------------------------------------------------------------gcatgttctcaaaaagcttacttcacaattaccaggttttggccacaga--gaaactaatagttcattt-ctttgggtggttt--------caatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
                                                                                    | |      |||||   || |||  |    |              ||||  |  |||  | | | |||  ||||    | |||        |||| |||||||||||||||||||| || ||||||||| |||| |||||||| |||||| ||||||| |||||| | |||| ||||
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttattcacttttaacgtttttgtttattcaatgtttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 13
------------------------------------------------gcatgttctcaa-----aaagcttacttcacaattaccaggttttggcca--cagagaaactaatagttcatttctttgggtggtttc--aatattt-cagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
                                                 ||| ||   ||      || || |  |||       ||| ||  ||     |        |  |  |  | ||  | | || | | |  ||  ||| |||||||| ||||||||||| |||||||||||||| || ||||| |||||  ||||||| |||||||| || | ||| 
gtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcagAATCTATATTGGGCTGACAGTGGTGATTTAGTAGCCATTGCTAGTGACACATCATTCTACATCTTGAAATTCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttcagAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT
               aactaat  putative branch site (score: 2)
                                         tttcaatattt  TA-rich tract