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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaacaagaaggacaagcttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacag

Basic information

species Vitis vinifera
transcript Vv11s0016g02430.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os05g51190.2 (Oryza sativa), 5'ss of exon 5
-----------------------GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaaca---agaaggacaagc------ttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacag
                       || |||||||||||  |||| || |||||||| |||||||||||||| || |||||| || ||||||| ||||||||||||      ||    |||| |      |  || | |   | |    || ||    | || ||||  ||  |  |  | | |      ||| |||
AAGTATCGTCATATCGTGTGCAGGTCGGAGATTTTGGGTTGGCTAGATGGCAGCCTGATGGAGACATGGGTGTCGAAACAAGAGTAATTGGCACATTTGGgtaagtgctcagccatacaatccatcaatcctgtcctttgtgaggtgtaacttgtgaaaaaggcatatctgag-accattttcggccatgtgcag

upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 5'ss of exon 7
GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaacaagaaggaca--agcttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacag
||||||||||||||  ||||| | ||||| || ||||| |||||||| || || ||  || ||||||||||||| ||||||| |   ||      | || |  | |   | ||     || |      | |    |   |  |  |    |||   | | | |||
GTTGGAGATTTTGGGTTGGCACGATGGCAACCTGATGGTGACATGGGTGTTGACACGAGAGTAATTGGAACATTCGGgtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttattaacgaggctctg---cttggctgtctgcag

upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G03340.2 (Glycine max), 5'ss of exon 5
GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaacaagaaggacaagcttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacag
|| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||  |  | || ||||||||||||||      || | |    ||     || | |    | ||| |  ||| ||||   |   || ||       ||  || |  ||||
GTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGGgtag-tgccaatgtcttttttcccattttcttttg-attagttgtaaaaaatgatgatgtaagcc-------ttggttattcacag

upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G36280.1 (Glycine max), 5'ss of exon 6
GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaacaagaaggacaagcttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacag
|| |||||||||||||| ||||||||||||||||||||||||||||| ||||||||  |  | || ||||||||||||||      ||   ||   ||     || | |    | ||| |  ||| ||||   |   ||||| ||  |  | | |        
GTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTGATAGGAACATTTGGgtag-tgccaatttcatttttcccattttcttttg-attagttgtaaaaaatgatgatgtaaacc-ttggttattcatag------

upper sequence: Vv11s0016g02430.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S59_359V6.1 (Physcomitrella patens), 5'ss of exon 6
GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaac-----------------aagaaggacaagcttttggcttccatcaatactagctaaaaataatggcaagtca--aaccattaatctt--acttttgtacag--------------------
||||||||||||||||| ||||| ||||| ||||||||| |    || ||||| ||  |  | ||||| || || |||||                    | | || | ||  || |   |  | ||  | ||| |  |    |   | | |        ||| | ||||  | |  || ||                      
GTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGGgtatgtgcccatcatctaatttaacgtagcataatattctaaatctcttcctttctaccccatgtcagacgtacgatgttgctcataattcttcgattcctgaacttttttgtggaatgtgttatag

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|30295608|gb|CB972402.1|CB972402
EST:     GAATAATTGGAACATTTGG                         GTACCTGTCTCCAGAATATGCTCAAAGTGGCCAAATCACAGAAAAAGCTGA
genomic: GAATAATTGGAACATTTGGgtaaacaaga ... ttttgtacagGTACCTGTCTCCAGAATATGCTCAAAGTGGCCAAATCACAGAAAAAGCTGA
EST: gi|30251712|gb|CB969445.1|CB969445
EST:     CAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG                         GTACCTGTCTCCAGAATATGCTCAAAGTGGCCAAATCACAGAAAAAGCTGA
genomic: CAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaacaaga ... ttttgtacagGTACCTGTCTCCAGAATATGCTCAAAGTGGCCAAATCACAGAAAAAGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGGgtaaacaagaaggacaagcttttggcttccatcaatactagctaaaaataatggcaagtcaaaccattaatcttacttttgtacag

- - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - -  AGTGGA