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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT

Basic information

species Vitis vinifera
transcript Vv08s0058g00390.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G05370.1 (Glycine max), 3'ss of exon 1
gtatgaaaatatgatttggaactgtg-atttttgtaatctgccttttttgtttttccaacatttttattgctgaacttc---ttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
    | ||   ||| ||  |  |||  ||| ||  | |     ||    ||||||  ||    ||| |  |||| |||     |   || |  |    | |||||| ||||| |||||||| |||||||||||||| |||||||| |||||||||||||||||||| || || |||||||||
----gtaatgctgagttttatttgtttattgttagacttgatattgaaggtttttttaattaatttgtgtctgagctttgaacttcaatatatgattgtaacagGCGAGAGGATTGAAGAAGCATTTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G43080.2 (Glycine max), 3'ss of exon 1
--gtatgaaaatatgatttggaactgtgatttttgtaatctgc-cttttttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
       |   | || |     | ||| |   |||   | ||    |||||||||        |||   ||  | |||||     | | ||  ||  ||||||||||| || |||||||| ||| | |||||||||||||| ||||||||||||||||||||||| || || |||||||||
ctaccataggttttggtcatttaatgtcagacttgctgtttgaatctttttgtttaatttgtgtttgagtt-ttaaactttcgtgcttatgactg--ttacagGCTAGGGGATTGAAGAAGCATCTCAAGAGGCTCAATGCTCCTAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G06170.1 (Glycine max), 3'ss of exon 1
gtatgaaaata-tgatttggaactg--tgatttttgtaatctgccttttttgtttttccaacatttttattg----ctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
     ||| ||  | |||| |  ||  |  || ||   |  |||  |||   |||||   |  || |  |||     | ||||| |   | | ||  ||  ||||||||||| ||  | ||||| |||||||| ||||||||||| ||||||||||||||||||||||| || || |||||||||
-----aaactagcgttttgtatatgatttgttctttagacttgctgtttagattttttttattttgtgcttgagctttaaacttttgtgcttatgattg--ttacagGCTAGGGGACTAAAGAAGCATTTGAAAAGGCTCAATGCTCCTAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G23730.1 (Glycine max), 3'ss of exon 1
gtatgaaaatatgatttgg--aactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaacttc---ttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
       | | | |||||   |    |   |||  || ||    |||||| |||||     |||||| ||  ||| |||     |   || |  |    | |||||| ||||| || ||||| ||| |||||||||| |||||||| |||||||||||||||||||| || || |||||||||
---cccgagttttatttgtttagtgttagatttgatattcaagattttttatttttaattaatttttgtt--tgagctttgaacttcaatttatgattgtaacagGCGAGAGGATTAAAGAAGCATCTGAAGAGGCTTAATGCCCCAAAGCATTGGATGCTTGACAAACTGGGTGGTGCATTT

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S461_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaact---tcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
   || ||   | |  |||    ||| |||  |   |     ||  ||| |  |     | ||| | |  ||  ||   |  |||       |||| ||  ||||| | || |||||||| ||| |||||||||||||||| || ||||||||||||||||||||| | || ||||| || 
-cctgcaagcttaaaatgggg--gtggtttagggttttgaagttggttgatgatgaggaagtttgagtcgtgttctgagttctgtttctcttgtgcgttttagGCTCGTGGTTTGAAGAAGCATCTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTTGACAAGTTGGGTGGTGCCTTC

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S39_422V6.2 (Physcomitrella patens), 3'ss of exon 1
--gtatgaaaatatgatttggaactgtgatt-tttgtaatctgccttttttgtttttccaacatttttattgctgaact-tcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
  |     | | |   | ||||  ||||    ||||| |  ||  |||| | |  |||| ||   ||     || |||| |  |||||      |   |  |||||| | ||  | ||||| ||||||||| | || |||||||||| |||||||||||| |||||| | || |||||||| 
aggcgaagacagaccctctggaggtgtgtcggtttgtcaattggattttctttgcttccgac--cttcggcacttaactatgatgtcacac--ttctttggcagGCTCGGGGTCTAAAGAAGCATTTGAAGCGACTGAATGCCCCTAGGCATTGGATGCTCGACAAGTTGGGTGGTGCATTC

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S2_16V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattg-ctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
 |  |   |  | |||     || | ||||||||  || |  | |    |   |       | | || | ||    |  |  || |     |   |  |||||| | || |||||||| |||||||||||||||||||| || | ||| ||||||||||||||| | || ||||| |||
tttcgtttacgtcattgttcgct-tcatttttgtggtcggtttatcgactggattttggcctgtcatggtctcctgtattcatctttccaatctctggcagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAGGCACTGGATGCTTGACAAGTTGGGTGGTGCCTTT

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S38_194V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgaaaatatgatttggaactgtgatttttgtaatctgccttt-tttgtttttc--caacatttttattgct--gaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
   | |     | |  |  |  ||   |  |||||    |  |   ||||||  |     || | |   ||| |  |||||  ||||  | | | ||   |  ||||| | || |||||||| |||||||||||||||||||| || |  |||||||||||||||||| | || ||||| || 
---ttatcggtttacgtaaacttgctttacttgtacgaagagtgcgtttgttcctgagtgacgtgtggcttgttacgaactaattgttttcttg-tgt-ctctagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCTCCCAGACATTGGATGCTTGACAAGTTGGGTGGTGCCTTC

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S81_172V6.1 (Physcomitrella patens), 3'ss of exon 1
-------gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
       || |   |  ||  ||| ||| ||||    |  |  | | | ||||||  ||||   || || || ||| |    || |||| || |   |    | |||||| | || |||||||| |||||||||||||||||||| || |||||||||||||| |||||  | || || || |||
gaggttggtttcgtagcatatttttgaaatgtg-cgctgatttttttcttttttttatttttttacgttgtttttgtt---ttttttgttattt---ttttcttcagGCTCGTGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCCAAGCATTGGATGCTCGACAAATTGGGTGGCGCCTTT

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S282_25V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgaaaatatgatttggaa-ctgtgatttttgtaatctgccttttttgtttttccaacatttttat-tgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
 |     | |  || |  |   ||  | | |||     ||| ||  |     | | |||    |   | |||| ||| | | ||   | | ||  ||| |||||| | || |||||||| |||||||||||||||||||| |||||||||||||||||||||||||| || || || || 
atgctggagtgagaatcagggtcttcggtattttgggactggctgatcaccctgttcaattggtacgtgtgctaaacatgt-gttgcg-gtgttgattccagGCTCGCGGTTTGAAGAAGCATTTGAAGAGGCTCAATGCGCCTAAGCATTGGATGCTTGACAAGCTGGGTGGCGCCTTC

upper sequence: Vv08s0058g00390.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ26570 (Selaginella moellendorffii), 3'ss of exon 1
gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
                                                ||     |  |     ||| || | |  ||||   ||    |||   | ||||   | |||  |||||| ||| |||||  |||||||||||| ||||||||||||||   |||||| || ||||| || 
------------------------------------------------gtgagagcg-cgcggctatcgcggga--tcttacgattcttgtgttgtgcagGTGCGCGGGCCGAAGAAGCATCTGAAGGTGCTCAATGCCCCCAAGCATTGGATGCTGAGCAAGCTCGGCGGTGCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT
           aacatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaaaatatgatttggaactgtgatttttgtaatctgccttttttgtttttccaacatttttattgctgaacttcttgtcatgtgggtgcattacagGCTAGAGGGTTGAAGAAACATTTGAAGAGGCTCAATGCCCCTAAGCATTGGATGCTTGACAAGCTTGGAGGTGCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg