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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatcacctttctccagttttatatattgccctttctgtgcatagaagcagcactgactttagtttaattaactctcccaatgcactagatagttg...

Basic information

species Vitis vinifera
transcript Vv04s0008g04410.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04410.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G10700.1 (Glycine max), 5'ss of exon 2
TATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatcacctttctccagttttatatattgccctttctgtgcatagaagcagcactgactttagtttaattaactctcccaatgcactagatagttg----
  | |||| ||| || |||||| ||||||| ||  ||    | ||  | ||||||||||||||| |||| |||||||||||  |||||||||| || |||||||| || | || | | |  | ||  | | ||  |  | || | |  |  | |    |||  |     || ||   |     | || |||  ||  |||    
CTTACCTGTGAAAGAGGTGCTTGAGAATTCTGGCCTGTCATTGGAACAAATATATGCAGTGGAGTTGATTGGAGGTGCCACCAGAGTGCCAAAATTACAGgtttgaataatctattttccttctttgacaatgtgcactttgggaagtgtgggatt--tgatctgcagatatttg--taaaatattgaactccatgcttgagag

upper sequence: Vv04s0008g04410.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G16070.1 (Glycine max), 5'ss of exon 2
TATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatcacctttctccagttttatatattgccctttctg-tgcataga-agcagcactgactttagtttaat--taactctcccaatgcactagatagttg
  | |||| ||| || |||||| || |||| ||  ||    | ||  | ||||||||||||||| |||| |||||||||||  |||||||||| || ||||||||  | |  ||  |     ||  |  |  |   | | || |    ||| ||| |||     || |  |  ||  |   |   | |   || | | |     
CTTACCTGTGAAAGAGGTGCTTGAGCATTCTGGCCTGTCATTGGAACAAATATATGCAGTGGAGTTGATTGGAGGTGCCACCAGAGTGCCAAAATTACAGgtttgattaatattctttttccttcgtcaacagtggtatttgatctgcagatagctgcatgatattgaactccatgcttgatagtcaacaacatttgttt----

upper sequence: Vv04s0008g04410.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G16660.1 (Arabidopsis thaliana), 5'ss of exon 4
TATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatcacctttctccagttttat-atattgccctttctgtgcatagaagcagcactgactttagtttaattaactctcccaatgcactagatagttg-------------------
||  |||   || || ||||| ||| |||||||||||||| ||||||| |||| ||||||||| || |||||||| || ||| |||| || ||  | |||||  |  |      |||| |     || |  ||| | ||    | || |   |  | |||   || | |||  ||  || | | |||| |    | |  |                    
TACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAGATTGATGATATATCTGCAGTGGAACTAATAGGAGGAGCTACTAGAGTTCCCAAACTACAGgtaggttttcatgctctcaaagccaatcaatttggcattctcatccaaaactgggggact---ttcactttttttttcttttcaaatgaagctaagatataatttttgttttaattacag

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|351026248|gb|FQ428260.1|FQ428260
EST:     TGTATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAG                         GCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
genomic: TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatca ... ctttttacagGCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
EST: gi|351030762|gb|FQ438600.1|FQ438600
EST:     TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAG                         GCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
genomic: TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatca ... ctttttacagGCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
EST: gi|110719052|gb|EE096589.1|EE096589
EST:     TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAG                         GCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
genomic: TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatca ... ctttttacagGCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
EST: gi|351021581|gb|FQ429685.1|FQ429685
EST:     TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAG                         GCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT
genomic: TATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatca ... ctttttacagGCAAAGCTCCAGGAATTTCTTGGAAGGAAGGATCTGGACAGACATCTGGAT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAGGTTGATGAGATATATGCAGTGGAGCTGATAGGAGGTGCCACTCGAGTGCCAAAGTTGCAGgtttgcatcacctttctccagttttatatattgccctttctgtgcatagaagcagcactgactttagtttaattaactctcccaatgcactagatagttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc