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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaattagaatcttggaaatcattcgaagatgacatttaaaaaaaaataaaaaaaaataataataaaaacgaatcttagcatcaatgaagc...

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 5
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaattagaatcttggaaat-cattcgaagatgacatttaaaaaaaaataaaaaaaaataataataaaaacgaatcttagcatcaatgaagc---
||||||| |||||||| || | ||||||  |||||||| | ||||| || |||||||||||||| ||||||||||| || |||||| | |   | || ||||     || ||| |    | ||||   | ||| |  | |   |    || ||||    || | ||||   | |   ||  |||  ||         |||    
TGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAGgtc----tgcaaagtgttcttttggttgtacatcctgatacagcgcacaataaaagtacaacagaaatttaattggcaaacaatagtatgcgaggaaaagtgta

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 5
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaattagaatcttggaaat-cattcgaagatgacatttaaaaaaaaataaaaaaaaataa--taataaaaacgaatcttagcatcaatgaagc--
||||||| |||||||| || ||||||||| |||||||| | ||||||||||||||||||||||| ||||| ||||| || || ||| | |   | || ||||  | |     ||||  |  | |   ||  |||| |    ||  |  | |||  ||   | |    |||  || |    |   |  |        |   | |  
TGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGAAGCTAGgtatgca-----attattacttggtggatatattcaatatcgagctgcataaaccaaatgatagtcttaagttatttggtagatacatgcatgcttacttatctt

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 3
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaattagaatcttggaaatcattcgaagatgacatttaaaaaa--aaataaaaa---aaaataa--taataaaaacgaatcttagcatcaatgaagc
||||||| |||||||| || ||| ||||| |||||||| | |||||||| |||||||||||||| ||||| ||||| || || ||| | |   | || ||||    |     ||||   | |||   ||   || || || |   | ||| ||   ||| | ||    || | |  || |  | ||    ||    |   ||     
TGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGAAGCTAGgt--acacaagtatta---ttttgtggatacatctaatatcaggctgaaataaccgaattataatcttaagttatttagtggatacatgcctgtttacttatttg--

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 5
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaattagaatcttggaa-atcattcgaagatgacat-ttaaaaaaaaataaaaaaaaataata-ataaaaacgaatcttagcatcaatgaagc-
|||| || |||||||| || ||  ||||| |||||||| | |||||||| |||||||||||||| ||||| ||||| || || ||| | |   | || ||||    ||| ||| ||   |||||  | |||    |  |  |     |||  |||  |||     |  || |  | | | | ||    |    | | | ||   
TGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGAAGCTAGgt----atgcaaagtactgtcttgatacatccagtggtgccggtgcattaccaaagcatatcttgagttatttcacatataggagctgtttacttatttaaatt

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G39870.1 (Glycine max), 5'ss of exon 5
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaatta-gaatcttggaaatcattcgaagatgacatttaaaaaaaaataaaaaa-aaataataataaaaacgaatcttagcatcaatgaagc
|| |||| ||||   | || ||||| ||| |||||||||| |||||||||||||| |||||||| ||||||||||| ||||| ||||| | | | || ||||| |  |     | | ||||  | || |           ||   | ||| |||| ||        ||   | | |||| |   |    | |  |  ||   
TGCTTGCAGCACTCACCATACAATTTGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGCACCTAAGTACCTTGCAGAGGCCAGgttcgcttttctttcatgaattgttgatacttactacttgtgttttctaataaaagatgttttttgaaatctgacaaaatctgctgcgggtagtagggag--

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA17G00910.1 (Glycine max), 5'ss of exon 5
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaatta-gaatcttggaaatcattcgaagatgacatttaaaaaaaaataaaaaaaaataataataaaaacgaatcttagcatcaatgaagc
|| |||| ||||   | || ||||| ||| |||||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||| | |   | || ||||| |  |     | | ||||  | || |            |   |   | |||| ||||       |||   | | ||    |  |      | ||    
TGCTTGCAGCACTCACCATACAATTCGGTCTCAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCAAATGCACCTAAGTACATTGCGGAGGCCAGgtttgcttttctttcatgaattgttgatacttaatacttgggctttccgataaaagataacgttttttaaatctgacaaaatctgctgcagatagtggga-

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37185119|gb|CF604472.1|CF604472
EST:     GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAG                         GAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
genomic: GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatgg ... ttatgaacagGAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
EST: gi|77584049|gb|DV221063.1|DV221063
EST:     GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATGTGCAAG                         GAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
genomic: GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatgg ... ttatgaacagGAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
EST: gi|77586184|gb|DV222186.1|DV222186
EST:     GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATGTGCAAG                         GAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
genomic: GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatgg ... ttatgaacagGAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
EST: gi|37190107|gb|CF609456.1|CF609456
EST:     CCTAAATACCTAGTACATGCAAG                         GAACGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
genomic: CCTAAATACCTAGTATATGCAAGgttagtatgg ... ttatgaacagGAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
EST: gi|71877133|gb|DT026188.1|DT026188
EST:     GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATGTGCAAG                         GAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
genomic: GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatgg ... ttatgaacagGAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
EST: gi|37186247|gb|CF605600.1|CF605600
EST:     GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATGTGCAAG                         GAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA
genomic: GGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatgg ... ttatgaacagGAATGGATCTCGATTAGGGCATGATACTATTGTTGATGGTATGATCAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTGCTGCACAGTCTATCCAATTGGGTGTCAATGATGTAGTTGTGGCTGGTGGCATGGAAAGTATGTCTAATGCGCCTAAATACCTAGTATATGCAAGgttagtatggaaattagaatcttggaaatcattcgaagatgacatttaaaaaaaaataaaaaaaaataataataaaaacgaatcttagcatcaatgaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa