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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA

Basic information

species Vitis vinifera
transcript Vv00s0125g00090.t01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os08g10300.1 (Oryza sativa), 3'ss of exon 23
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttcc--agTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
           | |  |   || |   ||   | | | | ||| |         || | ||       ||   ||||    || |  | | | |||    || |||||||||||||| |||||||||||| | || |||||||| || |||||||||||||| | |||||| || ||||||||||| |   |   |||  ||
----------gtatgcacatttcaccctt---tcttttcttatgag--------tttacctttgaagtctaagctaattttatctcgtctgaccttttgaagCGGCTATCTGGCACCCGAGTATGCAATGAGAGGCCATCTGACTGAAAAGGCTGATGTTTTCGCATTTGGAGTTGTTGCTCTAGAAACAGTTGCTGGCCGA

upper sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os08g10290.1 (Oryza sativa), 3'ss of exon 22
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
   | |     || |       | || ||     | || ||  ||  ||||| | | || |  ||  ||||  || | |               ||| ||||||||||||||||| |||||||||||| | || |||||||| || ||||| || ||||||| |||||| ||||| ||  | ||||   |   |||  ||
gtatgaacattttataccatgctcttattccgagtttatgttcaa-aacataacctaatatttttatcctcacctgacct-------------tttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGCCATCTGACTGAAAAGGCCGACGTTTTTGCATTTGGGGTAGTCGCCTTGGAGACTGTTGCTGGTCGA

upper sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os05g16824.1 (Oryza sativa), 3'ss of exon 22
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
             |     | || || |    | ||| | | |       || |||||   |    |     | |  |  | || | ||| |  ||| ||||||||||||||||| |||||||||||| | || | | |||| || |||||||||||||||| ||| || || || || || ||||   |   |||  | 
------------gtaagaacatttttatcatctctgttcttgtggc--tgtaacttcaa--aacaaaagctaatt--gtaacttgtctgtcattttcaagTGGCTATCTGGCACCCGAGTATGCAATGAGAGGTCGTTTGACTGAAAAGGCTGATGTTTTTGCATTCGGGGTGGTCGCGCTCGAGACTGTTGCTGGTCGG

upper sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os04g22470.1 (Oryza sativa), 3'ss of exon 19
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccacta--agccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
           |    |   ||||    |||  || |   ||| ||   |      |||| |  |||   | ||||  | |   | |||| |    ||  || |||||||| || ||||||||||||||| | || ||| || |||| |||||||||||||||| |||||| || |||   || ||||   ||  |||| ||
----------gtaagaacattttaccactgatcttct---tatgattgtaa-----catcaatatgaatcctactattaacttgtcttatat---ttttaagGGGCTATCTAGCTCCAGAGTATGCAATGAGAGGCCATTTGTCAGAAAAGGCTGATGTTTTTGCATTTGGAGTGGTTATGCTGGAGACTGTCGCTGGGCGA

upper sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os05g17050.1 (Oryza sativa), 3'ss of exon 27
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttcc---agTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
                      ||      |||    |  | |  | | | | ||  | || ||  |      |||     |  |  | | | |||     ||||| ||||| || || |||||||||||| | || | | ||||||| |||||||||||||||| |||||| ||                            
---------------------gtaagaacaaatcaacatttgtcttcatacaactataacttctaaatgaatgctacttttaactcgtttgatctttgtgaagTGGTTATCTAGCTCCTGAGTATGCAATGAGAGGTCGTTTGACAGAAAAGGCTGATGTTTTTGCATTTGGAGTG---------------------------

upper sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 22
lower sequence: LOC_Os05g16930.1 (Oryza sativa), 3'ss of exon 20
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
              | ||    | |       | | | | || ||   || || |  || |  ||| |  | | |||   | | |||| |     || || ||||| || || || |||||||||||| | || ||| || |||||||||| |||||||||| |||||| ||| ||    | ||||   |   |||  ||
-------------gtaagaacatttaaccatttctcttcttaaaaccgca-atatcaatatgattg-ctactattaattta-tcttatctttg--tcaagGGGCTACCTAGCTCCTGAGTATGCAATGAGAGGTCATTTGTCAGAGAAGGCCGATGTTTTTGCATTTGGAGTACTTATGTTGGAGACTGTTGCTGGTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA
                acttgac  putative branch site (score: 4)
                                                cttcc  putative PPT
                                   aattttatgtaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattcagtgaattttgaggctttattgttgaatttgtacgtataatgacatatcttcatctacttgacctccactaagccaattttatgtaaacttccagTGGCTATCTGGCACCAGAGTATGCAATGCGTGGGCATCTGACAGAGAAGGCTGATGTTTTTGGATTTGGCGTAGTTGCTCTAGAGATCCTCAGTGGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccactaa