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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgtttttaataatgcttttgcctaacaaactgattatattctgcatctttcaaactggcaaaatattacataagatattatgaa...

Basic information

species Vitis vinifera
transcript Vv05s0049g00960.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g41550.1 (Oryza sativa), 5'ss of exon 4
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgtttttaataatgcttttgcctaacaaactgattatattctgcatctttcaaactggcaaaat-attacataagatattatgaa---
 || || ||||||||| ||||||||||||| |||||||||||||| || || |||||| | |||||||| || |||||    ||| | || |  |||||||||||    ||  | |       ||  || |||||   |       |  |  |||   | |   || |    ||||   |   |   ||  | ||| |  |   
GCTATTGGATGCTGATCTGGAAAGTGATATTCTTGGTTGGCAGTACATATCTGGGAGCCTGCCTGATGGCCATGAGCTCAGTCGTCTTGATAATCCAGAGgtatgc--agtcactaaagcacaaa--atcctttttttttttttttttttgctatcaggtaagcttgattaaggcatgcttggtctttaccacattttcgatgg

upper sequence: Vv05s0049g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G172152_T01 (Zea mays), 5'ss of exon 4
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatg------ttgggtttccatgtttttaataatgcttttgcctaacaaactgattatattctgcatctttcaaactggcaaaatattacataagatattatgaa
 ||| | ||||| ||  | ||||||||||| |||||||||||||| || || ||||| || |||||||| || |||||    ||| | || |  |||||||||||      |  |         ||||   | |   | |  | | |   | |  ||    |   | ||| | ||    |  |   | | | |   || | ||   
GCTTCTGGATGCAGACCTAGAAAGTGATATTCTTGGTTGGCAGTACATATCTGGGAGTTTGCCTGATGGACATGAGCTCAGTCGTCTTGATAATCCAGAGgtatggaattgtaagaacaatgcattttagctcaaaatctcccttgaactattagttgatgtaaacctctgtgaactcag--attcactgc-tgttatttgat---

upper sequence: Vv05s0049g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G35220.1 (Glycine max), 5'ss of exon 3
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgtttttaataatgcttttgcctaacaaac-tgattatattctgcatctttcaaactggcaaaat--attacataagatattatgaa
|||| | ||||||||  | |||||||||||| | ||||||||||||||||||||  ||||||| ||||| || |||||||| || |||||||  || ||||| |||   |||| | |   || ||      |   |  |        | | |    | ||  | ||| | | |  | |  |  ||||  | | || || ||  
ACTTCTTGATGCTGACCTTGAAAGTGATATCTTGGGTTGGCAGTATATCTCAGGAGGCTTACCAGATGGCCATGAGCTTGAGCGCTTGGACAATCCGGAGgtttgtcatgttttccttcattcaaaggatttacagtttgcttggtatcactcagatgtgattattttatattccctagtttaattaatttaaat-ttctg--

upper sequence: Vv05s0049g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G32390.1 (Glycine max), 5'ss of exon 4
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgtttttaataatgcttttgcctaacaaac-tgattatattctgcatctttcaaactggcaaaatattacataagatattatgaa-
|||| | ||||| ||  | |||||||||||| | |||||||| |||||||||||  ||||||| ||||| || |||||||| || |||||||  || ||||| |||   |||| | |   || ||      |   |  |        | | |    | ||  | ||| | | |  | | |  |||| | |  |  |||| | 
ACTTCTGGATGCAGACCTTGAAAGTGATATCTTGGGTTGGCAATATATCTCAGGAGGCTTACCAGATGGCCATGAGCTTGAGCGCTTGGACAATCCTGAGgtttgtcatgttttccttcattcaaaggatttacagtttgcttggtatcactcagatgtgattattttatatt--ccatactttactttaatttctatgcat

upper sequence: Vv05s0049g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G00830.1 (Glycine max), 5'ss of exon 3
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgttt--ttaataatgcttttgcctaacaaactgattatattctgcatctttcaaactggcaaaatattacataagatattatgaa--
|||||| ||||| ||| | |||||||||||| | || |||||||| ||||||||  |||| |||||||| ||| ||||||| || ||||||   || | ||||||| | |||| | ||  |  | | |  | || ||  ||     |||   ||   |||     | ||| | |  || | | | |  |    |  | ||||  
ACTTTTGGATGCAGATCTTGAAAGTGATATCTTGGGCTGGCAGTACATCTCAGGCTGCTTGCCTGATGGCCACAAGCTTGAGCGCTTGGACGATCCTGCGgtatgtcgtgttttcttgactcataagttttactattttctttgtgact--ctaggatctaaggatctcacatt--catattttaatttctactcatttgaagt

upper sequence: Vv05s0049g00960.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G04400.1 (Arabidopsis thaliana), 5'ss of exon 4
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgtttttaa--taatgcttttgcctaacaaactgattatattctgcat---ctttcaaactggcaaaatattacataagatattatgaa----------------------------------------
|||||| ||||||||||||||| |||| |||||||| |||||||||||||| |||||  | || ||||| ||||||||||| || |||||||  || | ||||   |      |     || ||   ||    |     || |  | | | || |  | |||||    |||  |  |        |    ||  | | |  |  |                                        
ACTTTTGGATGCTGATTTGGAATGTGACATCCTTGGCTGGCAGTATATCTCTGGGAGTATCCCCGATGGCCACGAGCTTGATCGCTTGGACAATCCCGCGgtaaactacaaaacttgtcttatagtttagaattcaaagcttaataccagtttttgctatgcattcgttttttattttatttttcagcttatttggtttggttgatttagttctgaagtctatgaaaactctgtttttatttcag

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|33402515|gb|CF208142.1|CF208142
EST:     CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAATTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
EST: gi|37188201|gb|CF607550.1|CF607550
EST:     CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
EST: gi|33402247|gb|CF207874.1|CF207874
EST:     AGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAATTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: AGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
EST: gi|33402499|gb|CF208126.1|CF208126
EST:     CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAATTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
EST: gi|33402516|gb|CF208143.1|CF208143
EST:     CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAATTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
EST: gi|33402520|gb|CF208147.1|CF208147
EST:     CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAATTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
EST: gi|33402519|gb|CF208146.1|CF208146
EST:     CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAG                         ATTCAAGGCTCCAATTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG
genomic: CAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttggg ... ttctgagcagATTCAAGGCTCCAACTATGATCCAGAGGGTGAATATGTGAGACATTGGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTTTAGATGCTGATTTGGAAAGTGATATCCTTGGTTGGCAGTATATCTCAGGGAGCTTACCTGATGGTCACGAGCTTGACCGTTTGGACAGCCCAGAGgtatgttgggtttccatgtttttaataatgcttttgcctaacaaactgattatattctgcatctttcaaactggcaaaatattacataagatattatgaa

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcaaaa