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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagtggctggccttctgttctagctttcaaaacttaacattttaaagtttctcgtaaatagttacttaaaaagagtgaagttcaatttcaa...

Basic information

species Vitis vinifera
transcript Vv09s0002g07530.t01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GRMZM2G086030_T01 (Zea mays), 5'ss of exon 18
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagc-tagaagtggctggccttctgttctagctttcaaaacttaacattttaaagtttctcgtaaatagttacttaaaaagagtgaagttcaatttcaa------
|||| ||||| ||||| ||||| ||||| || || ||||| || ||||| ||| | || || || || ||||| || |||||||||||| ||||||| |||||||  | |   | | ||   || ||||  |||    ||||  |       |    |   | | ||  | |  ||   |  | |  |  ||  || |         
ATGAAAGGGAGCTTGGTCTTGATCATCCGGAAACTATGAAGAGTTATGGGGATTTATCTGTCTTCTATTATCGCCTTCAACACATTGAAATGGCTCTAAAgtaagtgtggttataggtg-ttttttgttgaagc----aaaaagtggtggcatggcatcaattgaaaccaat--ctgccatggtgctagtttatatctagccatcat

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA07G03250.1 (Glycine max), 5'ss of exon 19
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagtggctggccttctgttctagctt---tcaaaacttaacattttaaagtttctcgtaaatagttacttaaaaagagtgaagttcaatttcaa--
|||||||||| || ||||||||||| ||||| || |||||||||||||| |||||||| || ||||| |||||||| ||||||||||| |||||||||||||||| | ||      ||  ||  | |    | ||   | |  ||||     ||   | |||    | | || || || |   |     | ||    |||||   
ATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTTATTATCGTCTGCAACACATTGAGTTGGCTCTGAAgtaagttcgactatattgaactggtttagatgtttaagttatgactttctgcttgttattttgaaattactatttcctcattgatctaaatgtatcttttcacag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: GLYMA08G22850.1 (Glycine max), 5'ss of exon 17
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagtggctggccttctgttctagctttcaaaacttaacattttaaagtttctcgtaaatagttacttaa--aaagagtgaagttcaatttcaa----
||||||| || |||||||||||||| ||||| || |||||||||||||| |||||||| || ||||| |||||||| ||||||||||| |||||||||||||||| |  |  |   |||  ||   ||  |  ||| |    | ||  | |    |||  ||  ||||   || ||    |  ||   || |  |  ||       
ATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTTATTATCGTCTGCAACACATTGAGTTGGCTCTGAAgtaagttcaacttta-tggaattggtttagatgtttaagttatgaatttctgcttgttattctgaaattactattttctcattgatctaaatctatcttttgacag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 5'ss of exon 16
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagtggctggccttctgt-----tctagctttcaaaa-------cttaacatttta-----aagtttctcgtaaatagttacttaaaaagag--tgaagttcaatttcaa--------------------------------------------------------------------
||||||| |||||||| || |||||||| || || |||||||||||||| |||||||| || |||||||||||||| |||||  |||||||||| || ||||||| || |  ||  ||  ||  | |     | |||   | |||        ||||  | |||         || |   |   | ||| | |   ||  |  |   || |||  |                                                                       
ATGAGAGAGAACTTGGTCTCGACCATCCCGACACTATGAAAAGCTATGGGGATCTTTCTGTATTTTACTATCGTCTTCAACATTTTGAATTGGCACTAAAgtaagttatacatga-tgatctcttatagttatatagtcattaaagatggaaccttactactttgcttttccattacctttgtcttgttgccttggaatggcttatggtccaaccttttcctctgattggctccttttaaatatatctgccttctttctaaccatttttatttgttatctgttatag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 5'ss of exon 13
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagtggctggccttctgttctagctttcaaaact-taacattttaaagtttctcgtaaatagttacttaaaaagagt---gaagttcaatttcaa------------------------------------------------
||||| | |||||||| |||||||| || ||||| |||||||| ||||| |||||  |||| |||||||||||||| |||||||  || ||||| || ||||||| |  || |  |    |    |||     ||  | ||   |   |  | | ||| |||   | || |||| | |  |   ||   ||  ||  |  |  |                                                
ATGAGCGAGAACTTGGACTTGACCACCCAGATACCATGAAAAGTTATGGTGATCTGGCAGTATTTTACTATCGTCTTCAACACACCGAGTTGGCACTTAAgtaagttctaa-tacccaagcacaggtttctttttggagaatggtctaagatcagagtgtctttgagatcgttaatgattagttgttccgatttttgaactggaattatacgggaaggactgccgctcaatttttattttgttggaatgcag

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 5'ss of exon 18
lower sequence: EFJ24726 (Selaginella moellendorffii), 5'ss of exon 18
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagt---ggctggccttctgttctagctttcaaaacttaacattttaaagtttctcgtaaatagttacttaaaaagagtgaagttcaatttcaa
|||||||||| ||||| ||||||||||| |||||||||||||||||||| ||  |  | || ||||||||  | || ||||| |  || |||||  | | ||||  | |   |      | |  | || |  || |||   |                                                             
ATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTTACTACAGGCTTCAACATACAGAGTTGGCATTAAGgtaaagttgctcttttaagtagtgtactctattaacttctgaggtcag-------------------------------------------------------

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|110698822|gb|EE076760.1|EE076760
EST:     GATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAA                         GTATGTCAACCGCGCTTTATATCTTCTTCAGTTTACATGTGGACTGTCTCA
genomic: GATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctaga ... ttattggcagGTATGTCAACCGCGCTTTATATCTTCTTCAGTTTACATGTGGACTGTCTCA
EST: gi|32272114|gb|CD721273.1|CD721273
EST:     GATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAA                         GTATGTCAACCGCGCTTTATATCTTCT
genomic: GATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctaga ... ttattggcagGTATGTCAACCGCGCTTTATATCTTCT
EST: gi|32248906|gb|CD714725.1|CD714725
EST:     GATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAA                         GTATGTCAACCGCGCTTTATATCTTCTTCAGTTTACATGTGGACTGTCTCA
genomic: GATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctaga ... ttattggcagGTATGTCAACCGCGCTTTATATCTTCTTCAGTTTACATGTGGACTGTCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTTACTATCGTCTCCAACACATTGAATTGGCTCTGAAgtaagctagaagtggctggccttctgttctagctttcaaaacttaacattttaaagtttctcgtaaatagttacttaaaaagagtgaagttcaatttcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga