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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT

Basic information

species Vitis vinifera
transcript Vv06s0004g06860.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
-----gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
       | | ||  | ||      |    |  |    ||||||  |   ||   ||       |||| | |    ||| |  || | |||| ||||| || ||||| || ||||||||||| || ||||||||||  |||||||| || || || || |||||||| ||  ||||||| ||||||||||||
gtagttaactactcctgatgttgatatgtgcgaagc--aatttt--gtccttaacgtggcgcaccttaatatcgttctttacattca-acagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gta-tttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
||| ||   |  |    | |   | |    |       ||  |   ||   ||       |||| | |    ||| |  || | |||| ||||| || ||||| || ||||||||||| || ||||||||||  |||||||| || || || || |||||||| ||  ||||||| ||||||||||||
gtagttaactacacctgatgttgatatgtgcgaagcaattttgtccttaacgtggcgcaccttaatatcgttctttacattca-acagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
---gta-tttcttttaataaaag--aaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattt---tgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT----
   ||| ||||| ||  | | ||   ||   ||  ||  ||||||  |  | |||   | | |     |    | |  ||  |||   ||  ||||||||||||| |||||||| ||||| ||||| || ||||| || | |||||||||||| || || || |||| ||| ||  | || |||||||| ||||||    
caggtaatttctcttgctgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G102756_T01 (Zea mays), 3'ss of exon 4
gta-tttcttttaataaaa--gaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattt---tgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
||| ||||| ||  | | |  | ||   ||  ||  |||| |  |  | |||   | | |     |    | |  ||  |||   ||  ||||||||||||| |||||||| ||||| ||||| || ||||| || |||| ||||||||| || || || |||| ||| ||  | || |||||||| ||||||
gtaatttctcttgctgacagcggaatgcctttctcaaattatgcgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAAAATTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 6
gta-tttcttttaataaaa--gaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattt---tgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
||| ||||| ||  | | |  | ||   ||  ||  ||||||  |  | |||   | | |     |    | |  ||  |||   ||  ||||||||||||| |||||||| ||||| ||||| || ||||| || |  ||||||||||| || || || |||||||| ||  | || |||||||| ||||||
gtaatttctcttgttgacagcggaatgcctttctcaaattttgtgtgtctttctcaaaatgcaacacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGGACTGGACAAATCAAAGAAGTTGAACGTGTAACCAGAGAGTCAAACTTCTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
----------------gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtat---attttcttatttttcaccttcattttgag-acagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
                 |  |  |  || |     |     |  || ||||| ||||   || |    ||   ||    | || ||  |  ||| || |    | || ||||| || |||||||| ||||||||||| || |||||||| | ||||||||| || || || || || ||||| ||  | || || || || ||||||
gtagttactcttactcctgatgttggtatttcttaaggtggcataccttaatattaaat-ttctcaacatggcatgcattgatattaaattttctttatattcatagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 18
gtatttcttttaataaaagaaaaaactgactttaatttt-------aagcatt----------ttttgtatattttcttatttttcaccttc-attttg----agacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
|||||||||  || ||   |   |  ||||   | || |       ||  |||          || | | || |||  || ||||  | ||  ||| ||      |||| ||||| |||||||| |||||||| || ||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||
gtatttctt--aagaagcaatgtacatgacaccagttctctacacaaactattgcttttcaagttctatttacttttctaattttggctttttattctgtcttgtacagTGAGGATCCTGATATTCACTTCAAGTATATTGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 20
-----------------gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttc-attttg----agacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
                  | |   |   |  |       | ||  ||| |   |||     |||| | | || ||| ||| ||||  | ||  ||| ||      |||||||||| |||||||| |||||||| || || || |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||
gtatttcttaagaaacaatgtacatgacatcagttctccacacaaactattgcttttctagttttctatttacttttttaattttggctttttattctgtcttgtacagCGAGGATCCTGATATTCACTTCAAGTATATCGAAGCAGCTGCTAAAACTGGACAAATTAAGGAGGTGGAGCGTGTTACTCGGGAATCAAACTTTTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 20
gtatttcttt-taataaaagaaaaaac-tgactttaatt---------------ttaagcattttttgtatatt-ttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
|||||||||| | ||   |||   ||| |||| | | ||               || |   |||||| |  ||| || | ||||||    |||  | |   | || ||||| |||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||| || ||||| ||| | ||||||||||||||||||
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttgacttttttttttcaattattgtaattttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGACAAATTAAGGAGGTAGAGCGTGTAACTAGAGAATCAAACTTTTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 20
gtatttcttt-taataaaagaaaaaac-tgactttaatt---------------ttaagcattttttgtat------attttctta--tttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
|||||||||| | ||   |||   ||| |||| | | ||               || |   |||||| | |      |||||  ||  |||||    |||  | |   | || ||||| |||||||| |||||||| ||||||||||| |||||||||||||| |||||||||||||| || || || ||| | ||||||||||||||||||
gtatttctttcttattggagagtgaacatgacctcagttcactagttggtctgcttcactgttttttttttctttcaatttttgtaatttttttttgttctgtcttgtaaagTGAGGATCCTGATATTCACTTCAAGTACATTGAGGCCGCTGCTAAAACTGGGCAAATTAAGGAGGTAGAGCGCGTTACTAGAGAATCAAACTTTTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------------------------------------------------gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtat-----attttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
                                                                  ||||    |      |  || |    ||| |||    |  |  |  || || ||     ||   | || |   |    || ||||| | ||||||||||||||| ||||||| ||| ||||||||||| || || || ||||| ||||| ||||| || |||||||| ||  | || || ||||| |||  |
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgcatgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 20
gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
                                    | ||  | |  ||| || | || | | |  |  |   || | |     |||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| || ||| | || ||||| || ||||| ||  ||||||| || || ||||||
-----------------------------------gtatatccgtggttt-taaaattgcatgtaatcaagtgtcttgt----gcagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT

upper sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 20
gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
                                    | ||  | |  ||| || | || | | |  |  |   || | |    ||||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| || ||| | || ||||| || ||||| ||  ||||||| || || ||||||
-----------------------------------gtatatccgtggttt-taaagttgcatgtaatcaattgtcttgt----acagCGAGGACCCGGATATTCACTTCAAATATATTGAAGCAGCAGCTAAAACGGGCCAACTGAAAGAGGTAGAGCGTGTCACCAGGGAATCGAATTTCTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT
 ctttaat  putative branch site (score: 4)
                     tattttcttatttttc  putative PPT
     ttaagcattttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttttaataaaagaaaaaactgactttaattttaagcattttttgtatattttcttatttttcaccttcattttgagacagCGAGGACCCTGATATCCACTTCAAATACATTGAGGCAGCTGCTAAAACTGGACAAATTAAGGAGGTCGAACGTGTGACTCGGGAATCAAACTTTTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG