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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa...

Basic information

species Vitis vinifera
transcript Vv04s0008g02580.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 12
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttctt-ttgtcattatttattttattttttttctttctataagtaa-atcaa-ttgttaatattgaattgagaagtgtgatatatgcaa
|||||| ||||||||  | |||||||| || ||||||||||||||||| ||||| || ||||| |||||||| |||||||||||||| || ||| | |||||  ||||     ||||   |||  ||| |   |||| |    | | ||| | ||| | | ||  | || | |||  ||   || ||  ||    | |     
AATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGATTCTACTTCTCGGTGGGCTGAAGCTTTGCGTGAGATTTCAGGACGTCTGgtatgatgcttcctttcgagttgctattttacctttt-tggcctgtatttttgtaacttatattgacttctcaatgctgtgctgtgacatgaatgagaatt--

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 12
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattt--tttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa--
 || || || || |   | |||||||||||||||||||| |||||||| ||||| || || || ||||||||||| |||||||| || |||||  |  ||||  | ||   | |||||| || |||  ||    | ||||  ||||| | | | | |    |       ||||  ||| |   ||   |||  |||   ||   
GATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGGGCGTTTGgtacgttg---tttttcttctgccatacttgccctcatttcctttttgtatttctcatcctagtgtactttaac-ttgcacaaagctctgtcctattctcattg

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G128877_T03 (Zea mays), 5'ss of exon 9
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa-------------
||||||||| || ||| | || ||||| ||||| || ||||||||||| || || || || || ||||||||||||||||||||||| || ||  |  ||||  | |   |    |||| |||| | |        | ||  | | ||   |||||||||| ||  | ||| || | || || || |||  | ||   ||             
AATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctactca---tcttctgtcctca--------aattggtcttttaaaataagtaaat-aagagataacatagtatagaaaa-tgttttttaaataatctctggttcatc

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa----------
|||||| || || ||  | || ||||| ||||| |||||||||||||| || || || || || ||||||||||| ||||||||||| || ||  |  ||||  | |  |  || ||| |  |||      | ||  ||| ||||      |||||||||| ||  | | |||  |||   | || | | | | ||  ||          
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgtta-ctcatctctgtcctca------aattggtttcttttaaaataataagtaaat-aacagattata--gaaacaaaaattttaaaaaataaaatagtctctgg

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 13
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttatttttttt----ctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa
| | || || || || ||||| |||||||| ||||||||||||||||||||||| |||||| | ||||| || || |||||||| || |||||| |||||||||||     ||||||  |  |  || || ||     ||||        ||  | |  ||   | || |    || ||   |||  || | |   |||||   
ATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGACTGgtgaga-attttatttcagtaatagttgttcatcagtcttttagaaagatttcttttttgtgcttaaaatacagattttattttgt-aactttacaatatga--

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 13
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagat-ggcctatttcttttg-tcattatttattttattttttttctttctataagtaaatcaattgttaatattga---attgagaagtgtgatatatgcaa---------------------------------------------------------------------
| | || || || |||||||| |||||||| ||||||||||||||||||||||| |||||| | ||||| || || |||||||| || |||||| | |||||||||  |   ||||| || || | |  ||  || |  ||| |   ||| || || |  | | || | |   | ||||    || |        || |||  |                                                                      
ATTAGCTGAGTATTTTAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGGCTGgtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttccacag

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 13
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttc--ttttgtcat-----tatttattttattttttttctttctataagtaaatcaatt-gttaatattgaattgagaagtgtgatatatgcaa
||| || ||||| |||||||| ||||| |||||||| |||||||||||||| ||||| || |||||||| || || ||  | || || || ||| | ||||| |  |      ||||  |||||  ||     | ||  | || |  |  |      | |   |   ||| ||  || | |   | ||  |   |||  ||||     
AATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctatttt-gctttgttttatag----

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 13
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttatttt-attttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa-
  | || || ||||| || || ||||| || ||||||||||||||||| || ||||||||||| ||||| |||||| |  | || || || ||||| || ||  | |    ||     ||  |  | ||  ||||  ||   | ||||    ||   |      |   |  |   ||  || || | |||   || | ||  
CTTGGCGGAGTACTTCAGGGATATGGGGTATAATGTCAGTATGATGGCGGACTCAACATCTCGCTGGGCAGAGGCTCTTAGAGAAATTTCCGGAAGGCTTgtatgttcttataccatattcatt-taatagatttagatacgtgttctagtcattgttgttctgaccatccagtatgtctt-agcattgttggattttcatt

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 13
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattttttttctttctataagtaaatcaattgttaat--attgaattgagaagtgtgatatatgcaa---------------------------------------------
  | || |||||||| || || ||||||||||||||||||||||||||||| || |||||||| |||||||||||  | |||||||| |||||  |||| ||  | |  |     | |  | |  |  ||| |||    |||     || |     | |   | || || ||  |  | || |  | || |  |  ||||||                                             
TTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGGGCGACTTgtatgttctcaggactttcctttggtgttttttttagggtttcaaacttgttagtatcatgtatttatttatggacagtataggcaggttttgtccatgcaatgtcattcagactctaagacatgcagttactctgtggttttgcag

upper sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 13
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattt--tattttttttctttctataagtaaatcaattgtta-atattgaattgagaagtgtgatatatgcaa
  | || || ||||| ||||| ||||| || ||||||||||||||||| || || || ||||| ||||| |||||  | || || || |||||| |||| ||  | |    |    ||| |    |||||   ||  | || |||    |||||  ||| |||   |||    || || |  | |     |||   | | |||
TTTAGCAGAGTACTTCAGAGATATGGGGTATAATGTCAGTATGATGGCTGACTCTACGTCTCGCTGGGCAGAGGCCCTTCGAGAAATTTCTGGACGACTTgtatgtt--tttgcgccttgtactcttattagattattgttgtttgaacttctactagtcaattttttgaggcattttaagattattccagtggc-tgttcaa

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtaaa