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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

Basic information

species Vitis vinifera
transcript Vv08s0032g00600.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 8
gcatgtctttaccagtgtttctt------tactccgtcaactttattcttgggtaattgtgtactgatctggttaccttc--tcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
|  |||  |  |   |  ||  |      |  |  |  |  || |        |  |||| | |   | |   ||  ||   ||    |||     |||||||||| || | ||| ||||| ||||||||| |||||||||||||||| || || |||||||| ||||||||||| || || ||||| ||||| ||||| |
gtgtgttctacctgataattgatattgaatgatatgagatattgaactacatatgtttgttttcctgtttccgtaattttaatctcttttgggctgaacagTTGCCTCAAATAAATCCTGGTTTCAACAACGCTCCATTTAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTACATCCGTGAGAGTGATAAGGACA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
---------------------------gcatgtctttaccagtg-tttctttactccgtcaactttattc-ttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
                             | ||      || || |||  |   | |  ||| ||   || |   ||| || |||  | ||||  ||   ||||| |  ||| ||| |||||||||| || | ||||||||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||||| ||||| ||||| || |||||||| |
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctctt--ttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 12
gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
   | | |  ||   ||     |     |  ||| |      ||   |     | || |  | |  |||   |||  |  || | | |  ||| | ||||| || || |||||||| || | ||| ||  |||  || || ||  | |||||||| |||||||||||||| || |||||||||||||  || |
--gtatatacacacatgaacactggaagccccaagtcggccttttact-----tctattagttttattaatgtcttttttttctgtta--cagCTCCCACATACCAATCCTGGATTGAATACCACCCCGCTTAGGTTTACTAAGCATTCAAATGCTTACATGCTTGTGTACATTCGTGAAAGTGACAGAGAAA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 2
gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
   |  | ||     ||     |   ||  ||||    || |||| | | |||| |  | |  |   |    | || |  ||||||| |||||||||| || | ||||||||| ||||| ||||| |||||||||||||| || || || ||||| ||||||||||| ||||||||||| |||||||| ||||
--gtaacattctttatgacaaat-gttcattcaatacaatacttgcggacttgtat--taactttcctcttatttcttctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACGCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 12
--gcatgtctttaccagtgtttctttactccgtcaactttatt------cttgggtaa-ttgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
    |  ||||||  |   ||  || | | |   |   ||| |      ||||  ||| || |  ||| || || ||| ||  |  |  ||||||| |||||||||| || | ||||||||| ||||| ||||| ||||| |||||||| || || |||||||| ||||||||||| ||||||||||| | ||||||||| |
gtaaaattctttataacaattcattcaatacaatacagttacttgaggacttgtataaattttccacttat-tgcttaactcttattctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACACACCATTCAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTATATACGTGAGAATGACAAGGATA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G551402_T02 (Zea mays), 3'ss of exon 6
gcatgtctttaccagtgtttctttactc---cgtcaactttat----tcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
| | || | ||   || ||| |||| ||     | || | | |    |||     |  |   ||      | ||     | ||    ||| || |||||||| || || | ||||||||| ||||||||| ||||||||||||||||||| || ||||| || || |||||||| ||||| |||||||||| ||||||||
gtaagt-tctatttgtttttttttattcaaggataaattctgtgaagtctacctcatctacttatcaccatcgtctatgtttctcttttggattaaacagTTACCCCAAATAAACCCTGGTTTCAACAACGCTCCATTTAAATTCACGAAGTATTCAAACGCGTATATGCTTGTTTATATTCGTGAAAGTGCCAAGGAGA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 12
---gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
   |||     || | ||  |||||||| |       |||| || ||      || | ||||||  |   |  |   |   | || | |    ||||| || ||||  || ||||| ||||| ||  | || || |||||||| |||||||| ||||||||||||||||| ||||| || |||||||||||||| |
gtagcactctctttcgaggttttctttatttt-----ctttgttattt-----ttttttactgaatttactttcaaatttggtttctctt---cagTTACCGCAGAATAATCCTGGTTTCAATAATCCACCTTTCAAATTCACAAAATACTCGAATGCATACATGCTTGTTTATATTCGGGAAAGTGACAAGGATA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
---gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACA---CTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
     || |  || |     ||||  |  |  |  |||   | || |   |  |   |  ||||  |  || | |||   |  ||        ||| | |||||||| || ||||| ||||| || |   |||| || |||||||| || ||||| ||||| ||||||||||| ||||| || ||||||||||| |   
gttttattttcttgctccattttccatgatttg--aaccccaatcctaattcctctagc-ctgacatatttgctttcgtgtctttt-------cagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 12
--gcatgtctttaccagtgtttctttactccgtcaactttattcttgg----gtaattgtgtactgatc-tggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
      ||  |      | ||  | | ||   | |   || ||  | |    | || |     |    | |  ||      |  || |  |||    ||| | ||||| ||||| || || || || |||||||| || || ||||| ||||||||||| ||||||||| | ||||||||  | ||    |||||||| |
ttcagagtactagttgatattattatgctttatgatggttttttctagcgttgcaactaaaatccagccgtatttgtgcggtgatgttcttatcttgcagCTTCCACAAACAAATCCAGGTTTTAATAACACTCCCTTCAAGTTCACAAAATACTCAAACGCATACATGTTGGTGTATATCAGAGAGGCCGACAAGGACA

upper sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgt-actgatctggttaccttctcctgct-tgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
                                              ||||   ||| | | | || ||| |  |  | |  | | | |   ||||||||||||||| || || ||||| |||||| |||| || ||||| ||||| ||||| ||||||||||||||||| |||||  | || || || ||||| |
----------------------------------------------gtaagcatgtcattaaactagtttcggtgacttattgtttttcttacagTTGCCACAGACCAATCCCGGATTTAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA
                 tactgat  putative branch site (score: 2)
                               ccttctcctgcttgt  putative PPT
         taattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACACTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA