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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattacctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA

Basic information

species Vitis vinifera
transcript Vv03s0180g00120.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g02214.1 (Oryza sativa), 3'ss of exon 5
tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtatt---acctttttcacattcc--agggtttggttg--acagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
         |  |||  |    | |   |   | ||   ||||||| ||||  |   |||  || ||    ||||  |     ||||  |  ||||  |||  |||| ||  |||| || |||||||||||| | ||||||||||| ||||| ||||| || ||||||||||| || || |||||| ||||||||||||||||||| 
------agcttttaatgtac-acgacatcataagttacaagaaattgtttggaagaatgtcttgcatcctgacctcctgagttttccctattgttttattgggacagATTGTTAGGCGCTGTTGTTGTGATATCTGCAAATGCTGGGGGTGCATGGACACCAATTGGTGATGTGACGACCACTATGTTGTGGATTCATGGTCAGATT

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G053927_T02 (Zea mays), 3'ss of exon 5
tttctacattactaaaatgttgccaatcctctatttttcaga---aattctttgtcaacttgttctgtattacctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
      || | |||||  |       | ||| |  |   | |   ||| |||||      |||||| ||||   |   | | |        | | |  | ||| ||  |||| || |||||||| ||||| || |||||||| ||||| ||||| || ||||||||||| || || |||||| ||||||||||||||||||| 
-aatagcagt-ctaaagagcattttgttctccaaatccaacaatgaatactttggtggaatgttctttattgggtgagttaaacattgacttattgg-ggcagATTGTTAGGTGCTGTTGTTGTAATAGCAGCGAATGCTGGCGGTGCATGGACACCAATTGGTGATGTGACAACCACTATGTTGTGGATTCATGGTCAGATT

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G40920.1 (Glycine max), 3'ss of exon 5
----tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattacctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
     |||||  ||  | |  |  |   | ||  | | | ||  ||  ||      || ||| |    |  |    |  |    ||   || ||  ||||||||| | || ||||| |||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||| ||||||||||||||||| ||||| || |||
gaatcttctaagtt-ttcattttctagtattctccaactattttgaggtttggatacaccttatcaaatcctcaggtggttgattt---ggattctgttgacagGATTCTTGGAGCTGTTGTTGTAATAGCAGCAAATGCGGGGGGTGCATGGACTCCTATTGGTGATGTTACAACTACTATGCTGTGGATACATGGGCAAATA

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G26550.1 (Glycine max), 3'ss of exon 3
----tttctacattactaaaatgttgccaatcctctatttttcagaaattc-tttgtcaacttgttctgtattacctttttcacatt--ccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
     |||||  ||       ||||  || ||  | | | ||  ||  ||  | || | ||   ||   |  |  | |    |  ||     || ||   ||  |||| |  | ||||  |||||||| ||||| ||||||||||||||||| |||| ||| ||||||| ||||||||||||||||||||||||  |||| ||  ||
gaatcttctaagttttc----tgtt-tcattctccaactatttggaggtttgtctggctac--atttcatcatgtcatcaagaagttgatttggattctatttgcagGATATTGGGAGGTGTTGTTGTAATAGCAGCAAATGCTGGTGGTGCATGGAGTCCTATTGGTGCTGTTACCACTACTATGCTGTGGATAAATGGCCAAGTA

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G49810.1 (Arabidopsis thaliana), 3'ss of exon 3
---tttctacattactaaaatgttgccaatcctctatttttcagaaattctt-tgtcaacttgttctgtattacctttttcacattccagggtttggttgacagG-TTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
   ||| ||      |||||      |||| |||| | | |   | ||| |  ||| ||  |  | |  |      | |     ||| |         || || |  |  ||||||||||||| || ||||| |||||||| || || ||||||||||| |||||||||||||| || |||||||| ||||| ||||| || |||
tattttttattcccttaaaaa-----caattctctttatatggaacattatgatgtgaatgtcgtattaacgttagtatgtgtgttcaatataacctatggcaagACTTTTAGGAGCAGTTGTGGTTATAGCAGCAAATGCAGGAGGAGCTTGGACTCCTATTGGTGATGTTACTACAACTATGCTATGGATACATGGCCATATA

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G19490.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------tttcta-----cattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattac----ctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
                                                                         | || |     |||       ||||  | |    |  | ||||   | |    ||   |   |  |||||||||      |  ||   |  |           || |||  | |||||||  || || |||||||| |||||||| || || || |||||||| |||||||||||||| || |||||| | ||||||||||||||||||
gtatggaaaccttttcttaatgctctcctattagttagttagtttttgactccctacatatagaccttaagattctcaaggaaacatactggccatgtacctagagtttaaattttgttatacctcttacgataatactctgtattataacgttagtttgtacgctcaatgaccaatggcagACTTCTAGGAGGTGTGGTAGTGATAGCAGCAAATGCAGGAGGAGCATGGACTCCAATTGGTGATGTTACTACAACTATGTTATGGATTCATGGTCAGATA

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S246_109V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtatt-acctttttcacattccagggtttgg--------ttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
                                               ||    | ||  |  ||| |      |   | |||     |   |  |  |  || |||   ||| ||    |  || | | |  | || | ||        |    || || |||||||||||||||||||| || || ||||| |||||||||||||| || ||||| |||||||| || || ||||| ||||||||||| || || 
gtatacattatgtcggatcgcctttaggcacttcatggtattctctgttggcgcctttgttgaatatcttggtttggcaattgacatgcgctcatcaggaaagttgccttgtgtttgagtgatttataatttatggatgggggtggggctcattagATTTCTAGGAGCAGTTGTTGTGATCGCAGCCAATGCAGGTGGTGCTTGGACACCTATTGGGGATGTTACGACCACCATGCTTTGGATTCATGGGCATATT

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S298_28V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------------tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattacctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
                                                                                      ||| |  ||||      | |    | |  | | |  |   | |     ||| || ||  ||  |   |  ||  | ||       ||    | |  | || || ||||||||||| || ||||| || || ||| | |||||||| ||||| || ||||| |||||||| || || ||||||||||||||||| || || 
gtatgaatttcatccgactgtctgaagggttacgccttgatactttatggtagtcacatgtcactgatcctatgggcaaaattgcttttgttgattatctgggtttgataattgatatgtggtcacgtataaacttgccatct--ttgagagatttctgatccatgaatggggacgggctcaatagATTTCTAGGAGCAGTGGTGGTGATTGCAGCCAATTCAGGTGGTGCATGGACACCTATTGGGGATGTTACTACCACCATGCTGTGGATTCATGGCCATATT

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ16561 (Selaginella moellendorffii), 3'ss of exon 3
tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattacctttttcacattccagggt-ttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
                                               |  || |||   |||   | |   ||   | || |  |   |  | |||  |||| | || || || || ||||| || || || ||||| |||||||| ||||| || |||||||||||||| || || ||||| ||||| ||||| ||||| 
----------------------------------------------gtacgtaaac---ttccagacttttttcaccgcactaaatcctgctcgtttgcagGCTACTCGGCGCCGTAGTTGTCATTGCTGCGAATGCAGGTGGTGCCTGGACGCCTATTGGTGATGTTACGACCACCATGCTTTGGATCCATGGACAGATC

upper sequence: Vv03s0180g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ32271 (Selaginella moellendorffii), 3'ss of exon 3
tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattacctttttcacattccagggt-ttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
                                               |  || |||   |||   | |   ||   | || |  |   |  | |||   ||| | || || || || ||||| || || || ||||| |||||||| ||||| || |||||||||||||| || || ||||| ||||| ||||| ||||| 
----------------------------------------------gtacgtaaac---ttccagacttttttcaccgcaatatatcctgctcgtttgtagGCTACTCGGCGCCGTAGTTGTCATTGCTGCGAATGCAGGTGGTGCCTGGACGCCTATTGGTGATGTTACGACCACCATGCTTTGGATCCATGGACAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgtcaacttgttctgtattacctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA
                 tgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctacattactaaaatgttgccaatcctctatttttcagaaattctttgtcaacttgttctgtattacctttttcacattccagggtttggttgacagGTTCCTAGGAGCAGTTGTTGTGATAGCCGCAAATGCTGGTGGTGCTTGGACTCCCATTGGTGATGTTACCACTACTATGCTGTGGATTCATGGTCAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - actaaaa
- - - - - - - - - - - ccaatcc
- - - - - - - - - - - - - - - - - - - -agaaatt