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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt...

Basic information

species Vitis vinifera
transcript Vv06s0009g02730.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os03g25120.1 (Oryza sativa), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcat-cattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt-
||| || || ||| | || || ||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| || ||||||||||| |||||||| ||  |  || ||| |  | | | | | | | | | | | |  | |  |   | || |     | | |   | ||  |  | ||   |||  | |   | 
CTTCGTGGTGTGGCGGCCGCCGGAGTTCGCCAGGGACCTCCTCCCAAACTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTATgtaagcatatatacatcatgcatgtatatatatatatatatatgccgcaattaatttcactca--ttatgttatatgcatgctgtttttttcgctagctctt

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os07g44690.1 (Oryza sativa), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgag--agtgc-atcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt-
||| || || ||| | || || ||||| ||| | || ||||||||||||||||||||||||||||||||||||||||| || ||||||||||| |||||||| ||    ||| | ||||   | | | |  | |        | |  |||| |     ||      ||  |    |||   |||    ||   |  |||  || 
CTTCGTCGTGTGGCGGCCGCCGGAGTTCGCCCGCGACCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTATgtaagctgctgctaccattgcacatttttgccacatatatattgttgctctataagaatccgtaattttca----tgtcggtcaaaaacatgacggtggttgtg

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AC216247.3_FGT001 (Zea mays), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtg-catcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt
||| || || ||| | || || ||||| ||| |||| |||||||||| |||||||||||||||||||||||||||||| || ||||||||||| ||||| ||||| |    ||   ||    | | | | | | | | | | | | | | | | | | |  | |||   |     ||  |  |       | || | | | 
CTTCGTGGTGTGGCGGCCGCCGGAGTTCGCCCGGGACCTCCTCCCCAGCTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTACgtgagtgcaatatatgtatatatatatatatatatatatatatatatatatatatatatattaattagcggcgcatgcatgctgaggttatgatcgagtg-

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G025685_T01 (Zea mays), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccc-tctctctctctctctctctctctctctctctctctctcctg-attcaagcactgtgtttcatt--ttcacttcattgggggt
||| || || ||| | || || ||||| ||| | || |||||||| |||||||||||||||||||||||||||||||| || ||||||||||| ||||||||  |   | |  | ||   | |  |   | |    |   |  |  |   |  |  | | ||| || || |   |  ||| | ||  |  |  |  || |    
CTTCGTCGTGTGGCGCCCGCCCGAGTTCGCCCGCGACCTCCTCCCAAACTACTTCAAGCACAACAACTTCTCCAGCTTCGTCAGGCAGCTCAACACCTATgtacgtacgtagtagtattacattacatacacataatgcattgcattgcattgcattgtactgcatgcatggtttcagttcccttgctcgatcttgtttg----

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G36370.1 (Glycine max), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaag-cactgtgtttcattttcacttcattgggggt
 |||||||| ||||  ||||||||||||||||| ||||| || |||||||| ||||| |||||||||||||| |||||||||||||| ||||| |||||||| ||  | | |   |   | | | |   |||||      |    |||   ||| |       ||||   || || |||| |   | |     ||      
ATTTGTTGTGTGGAAGCCCCCTGAGTTTGCCAGAGATCTTCTTCCCAACTATTTCAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatccttatcttttcttatgtacttctctacaatccctattcttcatctttgcttcatttcacttcattgagtttgaaggtaaagctctttccat-

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA14G04070.1 (Glycine max), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt--
 ||||||||  |||| ||||| || ||||| || ||||| || |||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||||||||| | ||||  |  |  | | | |  || | |   |     ||| ||  ||  |  || ||   |   |    ||| |    |  | |          
ATTTGTTGTGAGGAGGCCCCCAGAATTTGCTAGAGATCTTCTTCCCAACTATTTCAAGCACAACAACTTCTCAAGCTTTGTTAGGCAGCTAAATACCTATgtgagaatccatctctt-ctatatatataacttttttggttctgatctatccttcattattgctttt-gtgatacacttcttgacaaagttagcctaatcat

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA02G44670.1 (Glycine max), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt--
 ||||||||  |||| ||||| |||||||| || ||||| || |||||||| ||||||||||| |||||||| ||||||||||||||||| ||||||||||||||| | ||||  |  |  | | | |  || | | | |     ||| ||  ||  |  || ||   |  ||    ||| |       | || |       
ATTTGTTGTGAGGAGGCCCCCAGAGTTTGCTAGAGATCTTCTTCCCAACTATTTCAAGCACAATAACTTCTCAAGCTTTGTTAGGCAGCTAAATACCTATgtgagaatccatctctt-ctatatatataactttttttgttctgatctatccttcattattgttttt-gtgctacacttcttgacagagttatagcctaatc

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA20G08250.1 (Glycine max), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagc--actgtgtttcattttcacttcattgggggt
 |||||||| ||||| |||||||||||||| || ||||| || |||||||| || || |||||||||||||| |||||||||||||| ||||| |||||||| ||  | | | ||     ||      ||   |  | ||| ||     ||    || | | ||| |     |  ||  || |   ||  |||||  |    
ATTTGTTGTCTGGAGGCCCCCTGAGTTTGCAAGAGATCTTCTTCCCAACTATTTTAAACACAACAACTTCTCAAGCTTTGTTAGGCAACTCAACACCTATgtaagcatcc-ttatcttttcttatgtacttctttacactccctactcttcatcttcacttcattgagtttgaaggtaattaaagatcttttcatgtgaac-

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S85_27V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagt-gcatcattaaccctctctctctctctctctctctc-tctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt
||| || |||||| | || ||||||||||| || |||||| | || |||||||||||||||||||| || |||||||| ||  |||| || || |||||||| ||    ||||   ||  |  |  |  || |     |    |  |||||| |     | |          | || |        |||  | |  | ||  
CTTCGTCGTTTGGCGTCCTCCTGAGTTTGCGAGAGATCTCTTGCCGAACTACTTCAAGCACAACAATTTTTCCAGCTTCGTGCGGCAACTAAACACCTATgtaagctccgcatttctacacaaccttgactattgtgatggaacgcctctctgttaacttaccagcatgtaaa-tgagacaaccgatcagataaaggagga-

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S12_41V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagt-gcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt
 || || || ||| | || ||||| || ||  | |||||  | ||||| |||||||||||||| |||||||| ||||| ||  | ||||| ||||||||||| ||    ||||       |    || | |   |  |      | |   |   |  |  |  | |  || | |   |    ||        |    |  |
ATTCGTCGTCTGGCGTCCTCCTGAATTCGCTCGAGATCTTTTGCCCAAATACTTCAAGCACAATAACTTCTCTAGCTTCGTACGACAGCTGAATACCTATgtaagctccgcattccgtttcgcaactgtgttgattgcgtgaaatttgattaattgccgtccaaat-gagtaatacatcaggttagtcaaagagaatgaat

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S19_153V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt--
||| || |||||| | || ||||||||||| || |||||| | |||||||| ||||| ||||||||||| |||||||||||  | || || ||||| ||||| ||  | |    || || |        |     |     |    |  |||| |    || | |   |   |  ||   |  | |  |||| | | ||   
CTTCGTCGTTTGGCGCCCTCCTGAGTTTGCGAGAGATCTCTTACCCAACTATTTCAAACACAACAACTTTTCCAGCTTTGTGCGACAACTAAATACTTATgtaagc-tccgcattttacacaaatatgatgataattcagatggagcgttctcacatagctaagtagcgt-ttcagtgagaagtgcgattcactcgaggaag

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S207_20V6.1 (Physcomitrella patens), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctga--ttcaagcactgtgtttcattttcacttcattgggggt
||| || || ||| |||| || ||||||||  ||||  | || || || |||||||||||||| || |||||||||||||||||||||||||| ||||| || ||         ||||    |  | |               ||    | |        |||  ||  |  |||  |  ||      ||  ||  |  || 
CTTCGTGGTCTGGCGACCGCCAGAGTTTGCACGGGACTTGCTTCCTAATTACTTCAAGCACAATAATTTCTCCAGCTTTGTTAGGCAGCTCAACACCTACgtaagtcgatccacttaagggacgttgtaaaatatcaggatgatcgagatttgagaaaggtgaaatttgaaaacta-ggctcgagaagacaccagggttgg-

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ15796 (Selaginella moellendorffii), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagt-gcat-cattaaccctctctctctctctctctctctctctctctctctctctcc-tgattcaagcactgtgtttcattttcact-tcattgggggt--------------------------------
 ||  | || ||| ||||||| || || |||| |||| || | || || |||||||||||||| ||||||||||| || ||  |||||||||| ||||| |||||  | |||| | ||  |  ||     |||    |   ||| |     ||  || ||   |  ||||    | ||  |    ||   || ||| ||  | |                                
GTTCATCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcgcatacgttttctttccacacctcctcatagttctttggagttcagtcccttagttcttcacttgcagtactcagcttcagctgtcaatgatgttgcccactgaacttcgttcttgtcgactcgcag

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ31857 (Selaginella moellendorffii), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctc-ctgattcaagcactgtgtttcattttcacttcat-tgggggt------------------------------------------
 || || || ||||  || || ||||| ||||  ||| | ||||||| |||||||||||||||||||||||| ||||| ||  |||||||||| || ||||||||  | |||    | | ||   |   ||  || ||| || |  ||  || ||| || ||  |||   ||| | |  |    |||  | | |    | ||                                          
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagt-tccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgtttgcttcgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ28850 (Selaginella moellendorffii), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctct-ctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt
||| || || ||||| || || ||||| ||| | ||  | ||||| |||||||||||||||||||| ||||||||||| ||  |||||||||| |||||||||||  |     || | |      ||||| ||   ||||        ||    | ||  |   |||  |||                             
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtgagtctctcgaatcaccttgaagctctcacttgttctccgatctgatcatcttatcgtcgcgttcttgcag----------------------------

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ38003 (Selaginella moellendorffii), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctc-ctgattcaagcactg--tgtttcattttcacttcattgggggt------------------------------------------
 || || || ||||  || || ||||| ||||  ||| | ||||||| |||||||||||||||||||||||| ||||| ||  |||||||||| || ||||||||  | |||    | | ||   |   ||  || ||| || |  ||  || ||| || ||  |||   ||| |   ||||   ||| |         | ||                                          
ATTCGTCGTGTGGAAGCCGCCCGAGTTCGCCACCGATTTGCTCCCCAGCTACTTCAAGCACAACAACTTCTCGAGCTTCGTCCGGCAGCTCAACACATATgtgagt-tccattccaagctcttgtttgttcgttcgctcgctttgccttcctatctttctctcgttcttccaccgagcgttttgctttgatccttgcaagagtctctctggcaactcactcacattgcaacaatgctgtgtgcag

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ17520 (Selaginella moellendorffii), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt
||| || || ||||| || || ||||| ||| | ||  | ||||| |||||||||||||||||||| ||||||||||| ||  |||||||||| |||||||| ||    |   | | ||| |  | ||||| ||   |||||       ||    | || |   |      | |                          
CTTCGTCGTGTGGAGGCCGCCAGAGTTCGCCCGCGACTTGCTCCCAAACTACTTCAAGCACAACAATTTCTCCAGCTTCGTGCGGCAGCTCAACACCTATgtaagt-ccctcgaatcaccttgacgctctcacttgttctctgatctgatcatcttatcattgctttcttgcag--------------------------

upper sequence: Vv06s0009g02730.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ32930 (Selaginella moellendorffii), 5'ss of exon 1
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctct-ctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcatt-ttcacttcattgggggt-----------------------------------------------------
 || || || ||| ||||||| || || |||| |||| || | || || |||||||||||||| ||||||||||| || ||  |||||||||| ||||| |||||  | |   |      || ||  | |   |||  |   ||| |     ||  || | |  |||     | ||  |  ||   |  |   | |  |  |                                                     
GTTCGTCGTCTGGCGACCCCCGGAATTCGCCAAGGATATCTTGCCGAATTACTTCAAGCACAATAACTTCTCCAGTTTCGTCCGGCAGCTCAACACCTACgtgagtctcccatacgttttctttccacacctcctccatagttctttggagttcagtcccttagttcttcgccagttgtcgatcacttgcagtactcagcttcagcattttgtcaatgatgttgcgcactgaacttcgttcttgtcgactcgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGTTGTTTGGAGACCCCCTGAGTTTGCCAGGGATCTCCTCCCCAACTACTTCAAGCACAACAACTTCTCCAGCTTTGTTAGGCAGCTCAATACCTATgtgagagtgcatcattaaccctctctctctctctctctctctctctctctctctctctcctgattcaagcactgtgtttcattttcacttcattgggggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc