Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagttgaatttggtgaaagattgagaaacatttatatactgaatgaatgctcaatgattattgcaatgttgcag

Basic information

species Vitis vinifera
transcript Vv08s0007g06710.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA09G16680.1 (Glycine max), 5'ss of exon 2
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagttgaatttggtgaaagattgagaaacatttatatactgaatgaatgctcaatgattattgcaatgttgcag---
 || || ||||| || |||  |||  |||||||||  ||||||| ||||||||| |||| |||||||||||||||||||||||||||  || | || |  ||||   | | |   | |||| | || | |||| ||| ||          |     ||| | |      ||  |    | || || ||| | |||        
CGACGGGTCGGTGACGGGGAAGAATTTGGAGTTGGAGGAAGGGATGTTGATTGTGCAGAGATGGAGGTTTGGGAGCTGGCCTGATGGGATTGAATCCATGgtaagaattatgaagc-ttgtgaatttatttgagtttagtattgtggcttgtggtttttgtgtgt--gctgtttttggattggtttttgtagtgtgatgtatg

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA02G28830.1 (Glycine max), 5'ss of exon 1
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagttgaatttggtgaaagattgagaaacatttatatactgaatgaatgctcaatgattattgc-aatgttgcag
|||||| ||||| || |||  |||  ||||||||| |||||||||| ||||||| |||  ||||||||||||||||||||| |||||  || | || |  ||||   | | |   | |||| | || | |||| | |   | | | | |      |||| | |    | ||  |    | || || | |  | || || | 
TGATGGGTCGGTGACCGGGAAGAATTTGGAGTTGGATGAAGGGAAGCTGATTGTGCAGGGATGGAGGTTTGGGAGCTGGCCGGATGGGATTGAATCCATGgtaagaattatgaagc-ttgtgaatttatttgagtgtttaggatggtgggttgtgatttttctgtgtactgtttttggattggttttggagagtgatgtat

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA03G30230.1 (Glycine max), 5'ss of exon 1
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagttgaatttggtgaaagattgagaaacatttatatactgaatgaatgctcaatgattat---tgcaatgttgcag
 ||||| ||||| || ||    ||  | ||||||   || || |||||||||||||||| |||||||||||| ||||||  |||||| ||| | || || ||||      | |||  | | | ||||  || |||  ||| | | |   | ||  ||||  ||  | |||||        |||||||   ||     ||||||
CGATGGGTCGGTTACTGGAACTAATTTAGAGTTGCAGGAGGGTAAGTTGATTGTTCAGAGATGGAGGTTTGGAAGCTGGAATGATGGAGTTCAATCCACAgtaa------gtgtttttgggt-tttgtattaaat--ggttagaaaaaaataatgattttaatcataaatgagaataatgtgattatctgtgtttatttgcag

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA19G33140.2 (Glycine max), 5'ss of exon 1
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaa----tgttcagggttccttgttatttga-gttgaatttggtgaaa--gattgagaaacatttatatactgaatgaatgctcaatgatt---attgcaatgttgcag
|||||| ||||| || ||    ||  ||||||||   || |  ||||| |||||||||| |||||||||||||||||||  |||||| ||| | || || ||||    | ||  || ||   | ||| |||      || ||| |||     | |    |||||  ||  || |  |||       || ||     |||     ||||||
TGATGGGTCGGTGACCGGAACTAATTTGGAGTTGCAGGAGGCTAAGTTAATTGTTCAGAGATGGAGGTTTGGGAGCTGGAATGATGGAGTTCAATCCACAgtaagtgttcttttggcttttgtattaattgttagaaaaattgatgattttaagtttttaacatgaatg-acagtgtgataatgtgataatctgggttgtgtatttgcag

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT3G12050.1 (Arabidopsis thaliana), 5'ss of exon 1
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagt---tgaatttggtgaaagatt-gagaaacatttatatactgaatgaatgctcaatgattattgcaatgttgcag
|||||| || || || ||  ||||  | ||| | |  ||||| || |||||||||||||| ||||| ||||||||||||||||||||| || |||| || || |  ||   |  |      |   | |     | |   || | | ||||| ||      || ||||| ||  ||  ||||     |||   |           
TGATGGGTCTGTTACTGGAATGAATCTTGAGCTTGAAGAAGGCAAATTGATTGTTCAGAAGTGGAGATTTGGGAGCTGGCCTGATGGTCTTGATTCAACGgttagtttagtgaatttggaatggctaaacgtattaccctgattatagatttgattgtggttgatatattggctgt-tgctttgacatttcag-----------

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|110362161|gb|EC925677.1|EC925677
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|33403213|gb|CF208840.1|CF208840
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|71874177|gb|DT023232.1|DT023232
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|30328084|gb|CD011346.1|CD011346
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|32268165|gb|CD717324.1|CD717324
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|71887065|gb|DT036120.1|DT036120
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|110383599|gb|EC947981.1|EC947981
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|30323537|gb|CD006799.1|CD006799
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTANACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
EST: gi|110373892|gb|EC938322.1|EC938322
EST:     TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACC                         GTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG
genomic: TTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttca ... aatgttgcagGTGCGAATTGCTTTTGATGAGCCTGAACCGGGGTTGACTGTTGTTAAACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGGATCGGTCACAGGGGTGAACATGGAGTTGGTTGAAGGGAAGTTGATTGTTCAGAAATGGAGGTTTGGGAGCTGGCCTGATGGTGTTAATTCTACCgtaatgttcagggttccttgttatttgagttgaatttggtgaaagattgagaaacatttatatactgaatgaatgctcaatgattattgcaatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT