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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattcttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g10680.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os11g40080.1 (Oryza sativa), 3'ss of exon 3
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattcttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                                                                | ||||   || ||| ||   |  | | |   | ||   | || |  |  |  |||| |  |||  ||| | |     |||    | |  || | | | |  ||||| |||||||| || |||||||||||  ||||||| || |||||||| || |  ||||| |||||| |||||||||| || |||
---------------------------------------------------------------aactgaaa--caattc-ataggaactagctgagttcacaaaaca-tgcaaaaagtattttaactta-acctaacaagtgcctacaatttatcaatataaatgtagGTCTGATGTTCTTGGCCAGTTCATGCCGCTGGTTGGTGTTGATTGGTCTCAAAATGGTGTTGCACATTTATTTTCTGCAATAAAG

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G154366_T01 (Zea mays), 3'ss of exon 4
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattcttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                                                         |  ||  |   ||| |     | |    | | || || ||||   |||||    ||  | |||      ||  |  | |   | |  || ||| |||   | | |||  ||||| |||||||| ||||||||||||||  | |||||||| |||||||| || |  || || || ||| |||||||||| || |||
--------------------------------------------------------atcattaaac--aatatggg--caagggcaatgtgattcatac---caccaactaatgttgtata-----ttaaaatcttacaaatgtttatgttttgtcatataattgtagGTCTGATGTTCTTGGGCAGTTCATGCCACTAGTTGGAGTTGATTGGTCCCAAAACGGAGTTGCTCATTTATTTTCTGCAATAAAG

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G04060.1 (Glycine max), 3'ss of exon 9
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattct-tattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                                                              | || || |    | | |||| |  ||   ||  |   |    ||  ||||| || | ||| |  || |    |   | |   ||| |||||  |  | | |||||||||||||||||| || |||||||||||| |||||||  | || ||||||||||||||||| |||||| |||| || ||||| |||
------------------------------------------------------------ccgaatagagtc---catgtattttgcttctcttc-tgttattttcaaaagatc-ta-actctagtatgaaattgt---aatttctttatcttgtttcatgtcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCTATCAAG

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G04230.1 (Glycine max), 3'ss of exon 10
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcatt-cttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                                                                | |  | | ||  ||| || |   |    || ||       ||  ||||| || | ||| |  || |    |   | | ||||| |||||  |   || |||||||||||||||||| || |||||||||||| |||||||  | || ||||||||||||||||| |||||| |||| || || || |||
-------------------------------------------------------------cctaatagagtccatgtcttttgtttctcttctgttat---tttcaaaagatc-ta-actctagtatgaaattgt--aatttctttt-tcttgtttcatttcttacagGTCAGATGTTCTTGGTCAGTTCATGCCTTTGGTTGGTATTGACTGGTCACAGACAGGTGTTGCACATTTATTCTCCGCAATCAAG

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G36130.1 (Glycine max), 3'ss of exon 5
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttggttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattct-tattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                                                                |||   || |||  || || |  |||  ||  | |   |   | |  ||  ||     | | |||      |   ||||  || || ||   || |   ||||||||||||||||||||| || ||||||||| | || ||| | ||||||||||||||||| || || ||| |||| || | ||| |||
---------------------------------------------------------------tattagtttccacaccttttct--tttcatttttgct--cttgatttaattctactcgatggtttgataatgttaaactc--ttcgttttattttatgccttacagGTCAGATGTTCTAGGTCAATTCATGCCTTTAGTAGGAATCGATTGGTCACAGACAGGAGTTGCTCATTTATTCTCAGATATCAAG

upper sequence: Vv18s0001g10680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G42870.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagggtactcaaatctttttctaaggttaaaaattgataccttgtatgttagatgtttttggattgaatttcacttctattatagtttg-gttgatacaagcaccagtagatcatatattcttgcttggacccatctgactccttttgtcttgcattcttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                                             |||    | |     || | ||  || | |  | | ||||| |||  |   |  | |  ||| ||      | | ||  || ||   |  |  |   |   ||| | ||   |  || |   || || |||||  |||| ||||| |||||| |||||||  ||||||||||||| ||||||||  ||||| | ||||| ||| | |||
---------------------------------------------gtaaagaaaaacacatttggttttatattatgttt-ttatattttaagccaagtccaaaacctgtt-----tctgtttctgattttccttacttactttgctttatattat-tgtttgtcgtagATCGGATGTATTAGGCCAGTTTATGCCTTTGGTTGGTATAGATTGGTCACAAACAGGTGTTACACATTTGTTTTCGGCTGTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatattcttgcttggacccatctgactccttttgtcttgcattcttattacagGTCAGATGTTCTAGGGCAGTTCATGCCTATGGTTGGAGTAGATTGGTCACAGACAGGTGTAGCACATCTATTTTCTGCTATTAAG
                     atctgac  putative branch site (score: 3)
                           ctccttttgtcttgca  CT-rich tract
                                          attcttatta  TA-rich tract