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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g07090.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 4
----------------------------------cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagc-taagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------
                                      | |   | ||| ||   ||| |   |||   || ||  | |   |  |  ||||      |     ||   || | |   |  |  | |||||| | |   |   | | | |   |  ||| | || || |      |||| || || ||||| ||||| ||||||||||| |||||||| |||||||| || || |                      
gtaaattacacccctacttggtacctcagtgtcatctacttgatatcac-atataatatttatttgcagacattcatta-gttgctagaggttcctgatgctccgagttgcttctgttgtatgtgttaccataattatgacatcttttactctctgtaactcattaaat------agGACAAATCATGGCGAGTTCGTTATATGGTTGCCAATCAATTGTATGAGCTCTGCGAGGCAGTTGGTCCTGAACATTCTAG

upper sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatt-taaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACAT-----ATTCCTCCCATAAATTATGAATTTCT-----CTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------
                                                  |   |   |  ||||   | | |||       ||||  ||||| | |    |||| | |     | |   |||      |     |||| | |         |   ||||     ||   | | ||   |||||  ||  |     |||||||||| ||||||||||| ||||||||||| ||||||||| | ||||| ||||||||||                      
gtatatcttacacacttttggtggcttaataaatgttgggagaaaagataaagttgtcaatacta-attctcgtaaa--aattactagagtaagatttccataagatctgctactagacaataatttcatgtgcttaagtttcagcacactaccatacatggttaatgatttcaattgcttatgttttcttaacatctcagGATAAATCTTGGCGTGTGCGCTATATGGTGGCAAATCAACTGTATGAACTATGTGAAGCTGTTGGTACTGAACCCACAAG

upper sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 4
cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------
                    | |||| ||| |          | ||| | | | || | |  |  ||||||            || ||||    ||| |     | || ||  | ||  | |  | | |    ||   | ||||||| || ||||||||||| ||||||||||| ||||||||||||||||| ||||| |                      
-------------------ttgtagttgctagag------gttgataatttcttagttttgcaacttgttgc-----------agttaagtg--catcaccactaacaaatgctacttgcttgtactct----tttgtttagGATAAATCATGGCGTGTTCGTTATATGGTTGCCAATCAATTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCTACAAG

upper sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------cgatcctaga---accactatgctatagtagcttggctactttag--taatagtatttaaggtataaattttgttgatacgcctt--taaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------
                                                       |  | ||   |  | |  |  | |     || | | ||  ||  | ||| | | |  |       | ||  |  | |  |||  |  || | ||    ||| |        | ||  | ||  |||| | |      ||   | ||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||||| |                      
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtg--cattaccgctgataaatgctacttgcatatactc---gctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG

upper sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 3
cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------
                                | ||| | || || | || ||  | | |     |  |  ||  || |  |||  | |  | | |    ||   ||||||| |       | |||||    | |    ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||                      
-----------------------------aaagttacat-agaaaaattaattttgcttttgccgtcttgtat-tgcttcgaaaaatgaatttctaca--tcttgtcacatagt-------tgaattact--tcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCC-TCCCATAAATTATGAATTTCT--CTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------
                                              |  ||  |  | | ||||  | ||| |    || |  ||    ||| |||  | |    |   | |||   || ||||    |   | ||||    ||||||||||| ||||||||||| || |||||||| |||||| ||||||||||||||||||                      
---------------------------------------------aaagatacatagaaaaaataattttgcttttgctgtctagtattgcttccaaaaatgaagttctacattttgtcacatagtagaattacttcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG
                     tgttgat  putative branch site (score: 4)
     tttaaggtataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgatcctagaaccactatgctatagtagcttggctactttagtaatagtatttaaggtataaattttgttgatacgcctttaaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG

- - - -agaacca
- - - - - - - ctatgct
- - - - - - - - - - - - - agcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagctaa