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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA

Basic information

species Vitis vinifera
transcript Vv13s0067g01290.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 10
------------------agaatcatgtt-tcatatagtcatggtggaaatttatactgttaaatcattatg----tagtctttgcatattt--------ggaatctgatagcctgcc--at-ttctatat--cagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
                  |   |  |||| | ||   || |   | | ||||||  ||  | |   ||  ||    ||    | |||||| |           || |||||||  |    || || |||||  |||||||| ||  | || |||||||||||||| || ||||| || ||||| || |||||| | ||||| |||||||| |||||  ||||||| || || || |
gtaagttccattacttctatgcttttgttgtgatgctgttacaattgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgttttatattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 10
------------------agaatcatgtt-tcatatagtcatggtggaaatttatactgttaaatcattatg----tagtctttgcatattt--------ggaatctgatagcctgcca-----tttctatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
                  |   |  |||| | ||   || |   | | ||||||  ||  | |   ||  ||    ||    | |||||| |           || |||||||  |        ||| |||  |||||||| ||  | || |||||||||||||| || ||||| || ||||| || |||||| | ||||| |||||||| |||||  ||||||| || || || |
gtaagttccattacttctatgcttttgttgtgatgctgttacaatcgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgctttatattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGAGA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
agaatcatgtttcatatagtcatggtggaaatttatactgtta-aatcattatgtagtctttgcatatttggaatctgatagcctgccatttc-----tatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
       ||| | |||   ||||     |   ||    | |||  ||   | ||| ||  ||   | | | | | |   || | ||||   |       ||  ||||| ||  | |||||||| ||| ||||||| || || |||||||| || || ||||||||||||||||| |||||||||||||| || || ||||| || |
------gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
--agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatat--cagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
  |     ||||||    |  | |  |      | | |  |||||    ||| | | ||  ||  ||   || ||| ||||  ||     | |  | ||  ||||| ||  | ||||| || ||| ||||||| || ||||| |||||||| ||||| |||||||| |||||||||||||||||||| || || || || ||||
tgattgctatgtttagcttcttaa--gaaatgctctctcttgttattgtatttt-tggttcttttattcatg-aatatgatgtccatatttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtcttt-gcatatttggaatctgatagcctgccatttc-----tatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
       ||| | |||   ||||     |   ||    | ||  ||   | |||  | ||| |  | | |   |     || | ||||   |       ||  ||||| ||  | |||||||| ||| ||||||| || ||||||||||| || || ||||| ||||||||||| ||||| |||||||| || || ||||| || |
------gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 10
-agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatat--cagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
   | |    |   |||||  | || |  |  | | |  |||||    ||| | | ||  ||  ||   ||||   ||||  ||   | | |  | ||  ||||| ||  | ||||| || ||| ||||||| || ||||| |||||||| ||||| || ||||| |||||||||||||||||||| || || || || ||||
tttacttcaatgcaatatacac-tgtttaatctctctcttgttattgtatttt-tggttcttttattcatgga-catgatgtccatacttgttgacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAACTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
----------agaatcatgtttcatatagtcatggtggaa-atttatac---tgttaaat--cattatgtag----------tctttgcatatttggaatctgatagcctgccatttctatatc--agGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
             ||||||  || | | |||  |||| |  | |||||    ||||||||  ||   || ||          || ||   ||||  |||  |  |    | |   |   || |   ||||||||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||||||||||||||| |||||||||||  | ||||| || |
gtatgcgatgtttatcatggatc-tgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 10
----agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
       |  |  | ||||| | || |  | ||  | || ||   |   ||    |  | |  ||  ||     |   || |||  |     ||  | |  |||||||||||||| |||||||| || |||||||| |||||||| |||||||||||||||||||||||||||||||| || || ||||| || ||||| || |
aacacttagtaaatatcataaactcct--tagacctctaaacccattgctcgaattacatttctta-atgcaaagttcctcatattcaatt-ttgatgttacagGTTGTCCAGCGGTTCCAAGAGTTATTTGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAGGGCATTCTACGGACACCTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattatgtagtctttgcatatttggaatctgatagcctgccatttctatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
                           atctgat  putative branch site (score: 4)
                                        ccatttct  putative PPT
                                          atttctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtctttgcatatttggaatctgatagcctgccatttctatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - tcatgtt
- - - - - - - - - - - tggtgga
- - - - - - - - - - - - - - - - - - - - - aaatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctgcc