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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT

Basic information

species Vitis vinifera
transcript Vv01s0011g02090.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatattttgttacttctttgt-caatggttttccattttaatgttttggtt--aaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
     |||     ||     |   | ||  | |  |    |||   |||    | || |  || |  |  | | || ||| |||  |||| ||   | || ||||||| ||||| ||||| |||||||| || || |||| |||||||||||||||||||||  | |||||||| || ||||||||||||||||| || ||| 
---aattatgcacatttgattattgtttataggcctgcgatgtccattccacattcagtatttgttaagctgagtgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatat---tttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
    |||   || || ||  ||    |    ||| |||     || ||  |  ||  ||||         || | |  |||   | | || |   || || ||||||| ||||| ||||| |||||||| || || |||| |||||||||||||||||||||  | |||||||| || ||||||||||||||||| || ||| 
---gcttctgattatgcacatttgattgtgttgtttataggcctgctatgtgctttccaataaccagtatttgttaaatttgtttcatatttcttatgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------attt-cttacaataatacatcttcagattccatgtatat-tttgt------tacttctttgtcaatggttttccattttaatgttttggtt--aaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
                                                     |||| |||  ||| || ||  |||   |    | ||||    ||        | | |    ||| |  || |  |  | | || ||| |||  |||| ||   | || ||||||| ||||| ||||| |||||||| || || |||| |||||||||||||||||||||  | |||||||| || ||||||||||||||||| || ||| 
gttttaaccattggtttgctgaatgtgtcttcagtgttgaaaaatttggacacatttgcttcaaattatgcacattcgactgttgtttataggcctgcgatgtccattccacattcagtatttgttaagctgactgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os07g26740.1 (Oryza sativa), 3'ss of exon 1
--atttcttacaataa-tacatcttcagattccatgtatattttgttacttctttgtcaatggt-tttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
  || |  ||    || ||   | | |||      | |   ||| |    |   |||||   || ||    |  || ||  |  ||||    ||   | |  ||||||| || ||||| || |||||||| || ||||||| |||||| ||||||||||||||  | |||||||| || ||||||||||| || || |||||| 
taatctgatattgcaaataaggcattagaaagtgagcactatttatg--cttaatgtcatctgtattcttgtagtattgaatatgttatcactgt--tttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTACACAAGGTTACCCAGTACAAGAAAGGAAAGGATAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttt-----tccattttaatgttttggttaaatgtggaa---tatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
      ||||      ||| |  |||       |||  |||| |  |   |||  || | | |     |   ||||||  |||    |   | |   |   |||| ||||||| ||||| ||||| |||||||| || || |||| ||||||||||| |||||||||  | |||||||| || ||||||||||||||||| |||||| 
------tacagc--cccatatggagaacttgcttatgctttggtcttcagttgctaaggatatgcaattttgttttaacctttgcaatttctttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAAGAAGCACACTCTCCACAAGGTTACTCAGTACAAGAAGGGTAAGGATAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G125527_T02 (Zea mays), 3'ss of exon 1
-atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaat-gtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
     || | |  ||    | || |  ||| ||  |    |   ||    |   |      | ||   ||   ||||   | ||   |       |||||||||||| ||||| ||||| |||||||| || || |||| ||| ||||||| |||||||||| | ||||||||||| ||||| |||||||| || |||||| 
tgaccctcatagaaagtgtttttta--ttcaattgactgctctctagagatggatatgaaatgttgttttaacatgtgcagtttgtttcacatgttatacagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACACTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G160351_T01 (Zea mays), 3'ss of exon 1
atttcttacaataatacatcttcagattcca-tgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatataca-------gGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
         | ||| |  | |||| ||   | | ||| |    | |||| |  ||  ||  | |     ||   |||   | | || | ||   || |||       |||||| ||||| || || |||||||| || ||||||| |||||| ||||||||||||||  |||||||||| || ||||||||||| ||||| |||||| 
------gggactaaaatttgttcatatattactttatttagcatgacttttcagtttattttatattgattctttgtg--gatgaattatgctgtacacatttcctagGTGAACGTTCCGAAAACCAAGAAGACCTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTGCACAAGGTTACCCAGTACAAGAAAGGTAAGGATAGCC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgt-tttggttaaatgtgga--atatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
                                                             ||   |||||||  |  ||    | | |  | |     |        ||   |||   |    ||||||  | | | |||   |    |   |||| ||||||| ||||| ||||| |||||||| || || |||| ||| ||||||| |||||||||  | ||||||||||| ||||| |||||||| || |||||| 
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagactcttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
-----atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
     |||   |   | | | |    |  | |   | ||    |||| || | |  ||  ||    ||   ||  |  |  ||| |||   |||| |     |||||||| ||||| || |||||||||||||| || ||||| ||||||||||||||||||||  |||||||||| || || ||||||||||||||||||||| 
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttccttttgtttgttgtgaa-----cagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatattttgttact-tctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
|||   |   ||   |  |  | |      || |     | ||| || |  | |  |||| |       |||  | ||||| |    ||   |||| | ||||||| ||||| || |||||||||||||| || ||||| ||||||||||||||||||||  |||||||||| || || |||||||||||||| |||||| 
attaggtttgattgaat-tggttattggttatttggtcatggttgctatgctggaaaatgttaaaatgcttttttcttttgttgttgtgaataataaatagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACGCTGCACAAGGTTACCCAATACAAGAAGGGTAAGGATAGCA

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatattttgttacttctttg--tcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
            |   ||||||||   | |||   |    | | |    ||||  | ||    | |  |||| |||  | | |||   |||    | | |||||||| ||||| |||||||||||||| || || ||||||||||||||||||||||||||  | |||||||| || || ||||||||||| || || ||| 
---------gtaagctcatcttcaatcttcatccctcaactctcatccgtttgattgaacaactcttgatttcaat--tatcgttttttgtttgct-tgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G08030.1 (Glycine max), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
                 | | |||  |||       | | |  | | | |   |  |   |||   |||| |||  | |||||   |      | | |||||||| ||||| |||||||||||||| || || ||||||||||||||||||||||||||  | |||||||| || || ||||||||||| || || ||| 
---------------gtaacctcatcttcttca---actctcatccgtttgattgcacaatttctgatttcaat--tatggtttgttt----gtttgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatatttt---gttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
  || | |   |||   || ||   |||     ||   ||    ||  |||  || |  |||  | |   |  |    ||||| ||   | || | | |  |||||||  |||||||||||||||| || || ||||||| |||||| ||||  ||||| || ||||||||||| || || ||||||||||||||||| ||  
-gttttcaatctaaatgatgtttgtattttgattaaccttaaaagtctcttgattttgtatgtgtgtgagtgattcatttttgattt--tatgaattttgaagGTGAACATTCCAAAGACAAAGAACACTTACTGTAAGAACAAGGAATGCAAAAAGCATACTTTGCACAAGGTTACCCAATACAAGAAGGGTAAAGACAGTC

upper sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G14320.1 (Arabidopsis thaliana), 3'ss of exon 1
atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggt-----taaatgtggaata-tacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
      | |   |   | | || |||||| |  | |||  |  || ||  || |  ||| | ||  |  |  || || ||||     ||||  |||  |  |  |||||||  |||| || || ||||| || || || |||| ||||||||||| |||||| || |||||||||||||| ||||| ||||| |||||||||||| 
-----gttctgaagggcgtatttagattc-acttctatgatcgtaattaattctgtatgctgttgaaactgtatcttgtggtagttttaaacttggttttctgtagGTGAACATTCCGAAAACTAAGAACACTTACTGCAAGAACAAGGAGTGCAAGAAGCATACCTTGCACAAGGTGACGCAGTATAAGAAAGGTAAAGATAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT
                      ttttaat  putative branch site (score: 3)
                     attttaatgttttggt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcttacaataatacatcttcagattccatgtatattttgttacttctttgtcaatggttttccattttaatgttttggttaaatgtggaatatacagGTGAATGTTCCAAAGACAAAGAAGACATATTGTAAGAGCAAGGAGTGCAGGAAGCACACATTGCACAAGGTGACACAGTACAAGAAGGGTAAAGATAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - -acaataa
- - - - - - - - catcttc
- - - - - - - - - - - - - - ccatgta