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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatatctatcctcaaatttagaattagtaagttctcagttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag

Basic information

species Vitis vinifera
transcript Vv00s0187g00030.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA18G01710.1 (Glycine max), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt----atatctatcctcaaatttaga----attagtaagttctc------agttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag---------------------
|||||||||||| |||||||| || || || |||||||||||||| ||||||||||||||| |||||||      ||  ||||| || |    |     |||  |  | | |      ||||| |     |||    |   |  ||||||       |  |  ||   ||||   |                     
GTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgattaatcctgaagtcctaattgctttaaaagatgcccttgactagttgttttttatgatgcatccttgacaagttctttaagcacttagtaa-aattatggttgtaccacttgacattgcag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G14050.1 (Glycine max), 5'ss of exon 9
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt---atatcta----tcctcaaatttaga-attagtaagttctcagttgctccaattgacctgttactatcaagtttaagtgtctttctgtggga-attgcag
|||||||||||| |||||||| || |||||  || |||||||||| ||||||||||||||| |||||||    ||| ||    |  |||||| ||   |||||| | ||   |     |||  |   | ||      |||     |      | ||     || ||||   
GTTTGTTGAGATTATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAGgttctttatttagtttttttcaaatatatctattagtta-ttgagaacaattcctgtatgcatgagcacttcatacccataaaaatatcaacatgacattg---

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G37770.1 (Glycine max), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgta---tatctatcctcaaatttagaat-tagtaagttctcagttgctccaattgacctgttactatcaagtttaagtgtcttt---ctgtgggaattgcag
|||||||||||| |||||||| || || ||  ||||||||||||| ||||||||||||||| |||||||    | |  ||||| || |    | | |  |||    |    |     | |||  || | |  |    ||  || | |  ||   |     ||  |||||
GTTTGTTGAGATTATGGCTCCAGTGTTCTCGCGAGATGCATGGCGCTGTGTGTGGCATATGATTCAGgttgactgttaatcctaaagtcctaattgttttaaaagatgtccttgataagttgttctttaagcacttggtaaaattatgattgtaccacttgacatgcag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G30850.1 (Glycine max), 5'ss of exon 9
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt---atatctatcctcaaatttagaattag-taagttctcagttgctccaattgacctgttactatcaagtttaagtgtctt--tctgtgggaattgcag--
|||||||||||| |||||||| || |||||  || |||||||||| ||||||||||||||| |||||||   ||   ||  ||  | || |   ||   |||  ||||  ||  |   |||||      | | |    ||  |   || |   |  |   |||  |||  
GTTTGTTGAGATAATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAGgttcaatggttactctttatttgatttttttctaatatctctattagtt--attgaga-acaattcttgcattagaacttcataccccataaaaatatcagcg

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G14040.1 (Glycine max), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt---atatctatcctcaaat----ttaga-----attagtaagtt------------ctcagttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag
 ||||||||||| |||||||| || |||||  ||||||||||||| ||||| ||||||||| |||||||   || | |   ||  | |    ||| |     ||| || ||||             | |   || |   || |  | | || || || | | | |||     | |||| ||| |||
ATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCGTTGTGTCTGGCATATGATTCAGgttaaatgttttctctttattctttttaaatatccattggttagttgtttaatgtctgtttaagcgcactcgttaaagtctaacaattaattatgattgttccattctgggcatttcag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G30830.1 (Glycine max), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgt---atatctatcctcaaattt------agaattagtaagtt-ctcagt---------tgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag
 ||||||||||| |||||||| || |||||  ||||||||||||  ||||||||||||||| |||||||   || | ||  ||  | | |      |  ||   |  |||  | | |         ||| |   ||    | | || || || | | | |||     | |||| ||| |||
ATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCATTGTGTGTGGCATATGATTCAGgttaaatgtttactctttattcttttttaaatatccattggttgtttaatgtctgtttatgcactcgttagagtctaacaattaattatgattgtaacattctgggcatttcag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatatctatcctcaaatttagaattagtaagttctcagttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag
 || || ||||| |||||||||||||| || |||||||||||||| || |||||||||||| | |||||     ||  || |  ||   |  || |   | ||   |  || ||  | |  | |   | |      ||| ||| | |       ||   |||
ATTCGTGGAGATAATGGCTCCTGTATTCTCAAGAGATGCATGGCGCTGCGTGTGGCATATGATCCAGgt-----tacacttactttattatctattggctccttcatatcttcatataatgtctccttcttgcacctaattgtatatgaaccaaaa--acag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatatctatcctcaaatttagaattagtaagttctcagttgctccaattgacctgtta---ctatcaagtttaagtgtctttctgtggg--aattgcag
 || || ||||||||||||||||||||||| ||| |||| ||||| || ||||||||| || | |||||    ||  | |||   |  |  | | |      |||  | | | || |  |   |     ||  |    |||   |  || |  |       |  |||
ATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAGgttc--cttgcttcatcatctgtttcattcttcattcatcttccctaactctctcttcttgcctgccttacttatacgctttaccttaaactgttaacag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT3G26440.4 (Arabidopsis thaliana), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatatctatcctcaaatttagaattagtaagttctcagttgctccaattgacct--gttactat-caagtttaagtgtctttc---tgtg-ggaattgcag---------------------------------------------------
                      || || |||||||| |||||||| ||||||||||||||| |||||  ||  ||    |||   || |  |   |    | |  | |     |||    |   ||||  || ||| |  || |   |  |    | |   ||||  |                                                    
---------------------AGTTTTCTCTAGAGAGGCATGGCGTTGTGTGTGGCATATGATTCAGA-ATGACTTGGTTCACGGTTGGGGTC--TTGACTTTGCGCTAAGAAAATGCGTCGAGgttaacatacaaatacaacttattcacaaacgcgtataattttacaaaacgttttcgaaactaagaagaaacactttttaatgattcaataaacag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatatctatc-------------ctcaaatttagaattagtaagttc--tcagttgctccaattgacctgt-tactatcaagtttaagtgt-ctttctgtgggaattgcag------------------------------------
                      ||||| || |||||||||||||| || |||||||||||| |||||    || |                ||  | ||   | |  |||| | |  | || |    || ||  |||   |||  | |   |||| |   ||     || |  | | |                                     
---------------------AGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTCGCACTCCGTAAATGCGTTGAGgttaatcattttgcctacataccttgactcttaaatacactggacatgtgtttggtaagttatctactaaaaagtttcctaataaaacaaacag

upper sequence: Vv00s0187g00030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 5'ss of exon 11
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatat--ctat--cctcaaatttagaattagtaagttctcagttgctccaattgacctg---ttactatcaagtttaagtgtctttctgtgggaattgcag
 ||||||||||||||||||||||| |||||  || | |||||||| ||  | ||| | ||  | |||||| ||  ||||  |||  |||   |  |         || ||  |   || | ||       ||   ||| | ||| | | |  || | |     || |||
ATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAGgtacattactatgaccttcaatgatgtgtcctctttaactgagacggaacactggagtgaggattttcatctaattttattattcttgt-tcctggttacag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAGgtatatctatcctcaaatttagaattagtaagttctcagttgctccaattgacctgttactatcaagtttaagtgtctttctgtgggaattgcag

- - - - - - - - - - - - - - - - GAGATG