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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTAATCGCTGCAAGGAATGAAGGAACACAGGTCACAATGGATCATTTTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatttttgacttattgcatttgttatatgattcttcgtctaatgttaagatgtttttgtcatgaacatatattttttttaatgctaattacttc...

Basic information

species Vitis vinifera
transcript Vv06s0004g05030.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G06530.1 (Glycine max), 5'ss of exon 6
TGCTTTAATCGCTGCAAGGAATGAAGGAACACAGGTCACAATGGATCATTTTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatttttgacttattgcatttgttatatgattcttcgtctaatgttaagatgtttttgtcatgaacatatattttttttaatgctaat-tacttc--
|||| | || ||||||||   |||||||||||| ||||||||||| |||||||||||||| || |||||||| ||||||||| |||| |||| ||| ||||||  || ||||    ||  |     | |||  |     |  ||   |||  | |  ||     |        | || ||| |  |||   ||| | | |   
TGCTCTGATTGCTGCAAGAGGTGAAGGAACACAAGTCACAATGGAACATTTTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtctttttaagttttatattactattaggtaggctt--gtgagatgggaggg-gtggagctgggtgttttttagtttataaaataagaatctgcatatc

upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G06580.1 (Glycine max), 5'ss of exon 3
TGCTTTAATCGCTGCAAGGAATGAAGGAACACAGGTCACAATGGATCATTTTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatttttgacttattgcatttgttatatgattcttcgtctaatgttaagatgtttttgtcatgaacatatattttttttaatgctaat-tacttc--
|||| | || ||||||||   |||||||||||| ||||| ||||| ||||||||||| || || |||||||| ||||||||| |||| |||| ||| ||||||  || ||||    ||  |     | |||  | |  ||| ||   |||   ||| ||     |        | || ||| |  |||   ||| | | |   
TGCTCTGATTGCTGCAAGAGGTGAAGGAACACAAGTCACCATGGAACATTTTGAGGCGGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtctttttaagttttatattactatta-gttacgctt-gtgagatgg-gagaggtggagctgggtgttttttagtttataaaataagaatctgcatatc

upper sequence: Vv06s0004g05030.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G14640.1 (Glycine max), 5'ss of exon 3
TGCTTTAATCGCTGCAAGGAATGAAGGAACACAGGTCACAATGGATCATTTTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatttttgacttattgcatttgttatatgattcttcgtctaatgttaagat--gtttttgtcatgaacatatattttttttaatgctaattacttc
|||| | || ||||||||   |||||||||||| || |||| ||| |||||||||||||| || |||||||| ||||||||  |||| |||| ||| | ||||  || ||||| | || ||  |||  |  || |     | ||   |||  | | |  |   | |   |       | |   | | |  |  | |||   |
TGCTCTGATTGCTGCAAGAGGTGAAGGAACACAAGTGACAAAGGAACATTTTGAGGCAGCCATTGATAGGATCATTGGTGGCTTGGAAAAGAGGAACAGGgtatgtc-tttttaagtt-ttatattactagtaggtaggcttgtgagatgggagggttggagctgggtgttttttactctgcatatcataggaagttatagc

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|110699287|gb|EE076153.1|EE076153
EST:     TTGAGGCAGCTATAGATACGATAATTGGTGGTCTGGAGAAGAAGA-TAAG                         GTGATAAGCCAGCTGGGAAGACGGACTGTTGCTTAACATGA-TCAGGTCAT
genomic: TTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatt ... tgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCAT
EST: gi|110365164|gb|EC928958.1|EC928958
EST:     TTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAG                         GTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCAT
genomic: TTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatt ... tgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTTAATCGCTGCAAGGAATGAAGGAACACAGGTCACAATGGATCATTTTGAGGCAGCTATAGATAGGATAATTGGTGGTCTGGAGAAGAAGAATAAGgtaactcatttttgacttattgcatttgttatatgattcttcgtctaatgttaagatgtttttgtcatgaacatatattttttttaatgctaattacttc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG