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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT

Basic information

species Vitis vinifera
transcript Vv14s0060g01680.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 4
----------actttacatatactgctgtgtgttacacgcatac-acacactcaaacatata-tgacctgttgtatcaaactctagtatgaatgagtccatggtg---tatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
          ||  || |  || |||| | |||||||   |||  ||    |  |   |  | ||   | || | | | |    |||    || | || |||  |   | ||||| || || |||||||| |||||||| ||||| || |||||||||||||| || ||||| || ||||| || ||||| ||  | ||  ||||||| |||| |
gtttgggaagacaatatac-tattgctatttgttacat-tatatgacctgtttgagtgttcactgtgattttctgttatatgtgagttc--ataattctatgacgacatttgcagCTTGAACTGGCAGCATCAGCTTTGTAAGAATCCTCGGCCAAATCCAGATATCAAGACTTTGTTCACTGATCATACCTGCACTCCGCCAAATGGAGCTCGT

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 4
actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaa---ctctagtatgaatgagt---ccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
              | |      ||  |  || |    |||  |||  ||||    | |    || ||    | |||| ||| ||| |   ||      | ||||| || ||||||||||| |||||||| |||||||| || ||||||||||| || || || |||||||| |||||||||||| | ||  | ||||| |||| |
--------------gtttgaaagtaatctaatgctgttactttaacggatattctgtttccattccaatatttttagtgtgactgatttcccccccaaatgtgcagCTTGAATTGGCAGCATCAGCTTTGTAAGAACCCTCGTCCAAATCCAGATATCAAAACTTTATTCACCGACCATACATGTTCTCCACCCAATGGAGCTCGT

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 3
-actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
 |  |  ||    ||   |   |   |    |    |||| ||     |   |    |    | |  |     | |||||     |||      | ||||| || ||||||||||| || | ||| ||||| || || ||||||||||| || || || |||||||| |||||||||||| |     | ||||| |||| |
cagctagcaccccctctcgcacggccctgttac-tgcacattctgttttcgttccgttacaatttttattgtgattatgatgccctccccaaaatgtgcagCTTGAATTGGCAGCATCAACATTGTAAGAATCCTCGTCCAAATCCAGATATCAAAACTTTATTCACTGACCATACATGTACTTTACCCAATGGAGCTCCT

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 4
-actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
 | | ||  |    |  | |   ||  | | ||    |   | ||     |||| | | |  |  |      ||       || |||| |  |  |||||||||||||||||| |||||||||||||| |||||  |||||||||| || || ||||| |||||||| ||||| |||||| | ||| | |||||  |||| 
gattatatgttatttattattaatttaatgtatttg-atttttaacttgctatgccttatcattgcttttattaaccgatttgtgtccctaatcaatgcagTTTAAATTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 4
actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
  |     | || | |  | |  || |     |     |        |   |  ||| || | | |      | | |   |  | || |  |  ||||||| |||| |||||||| ||||| ||||| |||||  ||||||||||||| |||||||| ||||||||||| || |||||||| ||| | |||||  |||| 
gttccttttttaattcattcttgtaaatttgaatttttagcgtgctgtgccttgcctattttttaatcagtgaatttatctatgccccttatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCCAATGGTCCTCTG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 4
actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
| |     | ||      | |  || |  |  |     |       ||   |  ||| || | | |      | | |   |  | ||||  |  ||||||| |||| |||||||| ||||| ||||| |||||  ||||||||||||| |||||||| ||||||||||| || |||||||| ||| | |||||  |||| 
attccttttttaaatgattcttgtaaattcgaatttttagcttgctatgccttgcctattttttaatcagtgaatttatctatgcccattatcaatgcagTCTAAACTGGCAGCATCAGCTCTGCAAAAACCCAAGGCCAAATCCAGATATTAAGACTTTATTCACAGATCACACATGTGCACCTCCTAATGGTCCTCTG

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 5
-actttacat-atactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
   ||||  | ||  |  | | ||||  |   ||  | |   | ||     |||| | |||  |  |      ||       ||  ||| |  |  |||||||||||| ||||| |||||||||||||| |||||  |||||||||| || || ||||| |||||||| ||||| |||||| | ||| | |||||  |||| 
ggttttaattgattatattat-tgtttaataaattta-atttttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 4
--------actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacct-gttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
          |||   | | ||  ||    ||       |   || | | |    |  ||||| | |||||   |   |  | | || ||  || |        |||||  | ||||||||||||||| | |||||||| ||  ||||||| ||||| ||||| ||  ||||||||||||| || ||  | | | | |||||  |||| 
gtgtgtttcttttttctttcctcatgaccattctgtatgt-tgcaga-tgaggtttggatgacttcgttgttggatgattcattgtgcatatgttctct-----tgcagCCTCAATTGGCAGCACCAGTTGTGCAAGAATCCTAGGCCAAACCCAGATATTAAAACTCTATTCACAGACCACACTTGCACACTTCCGAATGGTCCTCTC

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------actttacatatactgctgtgtgttacac-gca-----tacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
                                                                      |   |||     |  |  ||  |||| |||     ||    |  || ||   |   ||    |   || ||    |  ||||  |  ||  ||  | | |||||| | ||||||||||| ||||||||||| |||||  |||| ||||| |||||||||||| | ||||  || || ||||| |  ||| | ||||||||||  
gtaataaatagcccatgtgttctaccttgagctcctcaagattatccaggtggtggcttctgcttgtagttgagcattgttggtggcatgcaacaccgcactttgtattttccttcgaattcaccagagtattgacatgaaggatttttatgtgttcgtttatc-tatttgcagTCTCAATTGGCAGCATCAGCTTTGCAAAAACCCAAGGCCGAATCCTGACATTAAGACACTCTTCATTGATCACACATGCGGGCCTCCTAATGGGGCTCGA

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 4
actttacatatactgctgtgt-gttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgta----tgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
  ||| ||     |  ||||| |||  |   || |      |   || || ||||    ||  || | | |   |  |   || |   ||  |||     |||||| | || ||||||||||||||||||||||||||  |||| ||||| ||||| |||||| | || |  || || || ||||  ||| | ||||| || | |
--ttttcaacgtttcatgtgttgttttaaatattcttttcattgtactta-atgagaatttaaataagaatt--gctttcttgtgcttattttgttaccctgcagTCTCAACTGGCAGCACCAGCTTTGCAAGAACCCAAGGCCGAATCCTGACATCAAGACACTGTTTATTGATCACACTTGTGGACCTCCTAATGGTGCCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
                tatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttacatatactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT

- - - - - -actgctg
- - - - - - - - - - - - acacgca
- - - - - - - - - - - - - - - - acacaca
- - - - - - - - - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtccatg