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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttttttggcagttcaggtttgattagtttggtttcaagtcgtcggatcttgagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG

Basic information

species Vitis vinifera
transcript Vv01s0011g02270.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 1
------------------------ttagttttttg-gcagttcaggtttgattagt-ttggtttcaagtcg----tcggatcttgagtgt-cattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
                        |  | |    | | | |||  |||    | || ||  |||   ||      |||     ||| |||     | | ||   |     |   |          || |||||||| |||||||| || || || ||||||||||| ||||| ||||||||  | ||  |||| ||||||||||| || || || || ||||| || ||||
gtgagtgttccggagcctaccgcctcggatccgggtggaattcgtgttctggtggtgttaattttgggtttggtttcgctcactgactgtgtgcatgggtggggggggggggggtgtgggggccggtgcagATGCTCGGAGATGAAATAGGGAAGGGAGCATATGGGCGAGTGTACAAGGGGCTTGACCTGGAAAATGGAGACTTCGTGGCCATCAAGCAAGTATCGTTGG

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G03090.1 (Glycine max), 3'ss of exon 1
ttagttttttggcagttcaggtttgatt--agtttggttt--caagtcgtcggatctt-gagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
 |  | |||      ||||  ||  ||    |  ||| |    || | |  |||| || || || |    ||||  || | | ||  ||  |  |||  |  |||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||||||  ||||||||||||| |||||||| |||||||||||||||||||
gtcttgtttctattcttcaaattgtatatgggactggatcactaaatagctggatttttgaatggc----tgattgctttgtttgcatttgagatttg-gagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G10810.1 (Glycine max), 3'ss of exon 1
ttagttttttggcagttcaggtttgattagtttggtttcaagtcgtcggatcttgagtgtcattttgatgtctg--tatatgatttccattt----ttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
 |  | ||||     || |  ||  ||     |||  |    ||   | ||   |  ||   |||| ||| |||  |   |  |||  || |    ||| |  |||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||||||  ||||||||||||| |||||||| |||||||||||||||||||
gtgttgtttttattctttaaattgtata----tggaattggatcactgaata--gcttgattttttaatggctgattgctttgtttgtatgtgagatttggagcagATGCTGGGAGATGAGATTGGAAAAGGAGCTTATGGTCGAGTTTACAAAGGTTTGGACCTGGAGAATGGAGATTTTGTTGCCATTAAACAAGTTTCTTTGG

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 3'ss of exon 1
-----ttagttttttggcagttcaggtttgattagt-ttggtttcaagtcgtcggatcttgagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
     || |  |  |    |||     || |||  | ||||||||| ||  |||   || |  |    || || | | |  ||  ||     ||| | |    ||||||||||| ||||| ||||||||||| |||||||| ||||| ||||| ||  |||| ||||||||||| || ||||| || ||||| || || ||  |||
cagatttggcctcctacttgttg----ttaattgctattggtttcatgtactcgaggctggctttcatttctgcttttttgatccgacga--attgtatctggcagATGCTTGGTGATGAAATCGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGATTTTGTGGCTATTAAGCAGGTCTCACTGG

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S99_12V6.1 (Physcomitrella patens), 3'ss of exon 1
----ttagttttttggcagt---tcaggtttgattagtttggtttcaagtcgtcggatcttgagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
          |     || |   |    | ||  |  |   |   |   |  | | |||  | |    | | |||||||   ||||| |||    |  || |  ||| |||| |||||||| ||||| ||||| |||||||| ||||| |||||||| ||||||||||| |||||||| ||||| || || ||||| |||||  |||
acatacgaactagcaacaatcgctggtatctggcttttccagagactcttacttgcatccagtgatgtaatatgatgtc---atatggttt--gatggttgg--cagTTGCTGGGAGATGAAATCGGTAAAGGGGCATATGGCCGAGTGTACAAGGGATTGGATTTGGACAATGGAGATTTTGTGGCGATCAAACAGGTTTCGCTGG

upper sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 1
-ttagttttttggcagttcaggtttgattagtttggtttcaagtcgtcggatcttgagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
   |  | ||   | | |    |||||     || |  ||||   ||| ||  ||   | |  |  |  |||||  |  |     | ||| | ||   ||||||||||| || || || |||||||| |||||||| ||||| ||||| ||  |||| ||||||||||| |||||||| || |||||||| || || ||||
gggatatgttctcctgcttgtttttgagattctttggctcaatgtgtcagaatttagcttttctgctagtgtcttgactttgac-caattgtatttggcagATGCTTGGTGACGAAATTGGAAAAGGTGCATATGGGCGAGTGTACAAAGGGCTGGACTTGGAGAATGGCGACTTTGTGGCCATTAAACAGGTCTCATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggatcttgagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG
                 ttttgat  putative branch site (score: 4)
                                    tttccatttttttgtt  putative PPT
                                   atttccattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttttttggcagttcaggtttgattagtttggtttcaagtcgtcggatcttgagtgtcattttgatgtctgtatatgatttccatttttttgttcagATGCTTGGAGATGAGATCGGAAAAGGAGCATATGGTCGAGTTTACAAGGGTTTGGATTTGGAGAATGGAGACTTTGTTGCAATTAAACAAGTTTCTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - -tcaagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtctgt