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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatccagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttatcag

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 7
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttca-tccagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttatcag-----------------------------------------------------------------
|| |||||||| || || ||||| ||| | ||||||||||| ||||| ||||||||||||| || | | |   |||   |  ||| |   |  || | | |  | || | | | ||       | |||   ||| |      ||  |                                                                 
GTTAACCCACATACACACCAGCTCAAAATATGTGATTTTGGCAGTGCAAAAGTTTTGgtaagttctgaatttggca---gaaatttaaattcacaagcatttctgttttctgaatggacacactgggttttcttgcaaggaaatgtgaacttaggcaggtagcctacacatgatagtcttaaattgcagctttttccccgccgaatgtgcag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA16G00400.1 (Glycine max), 5'ss of exon 6
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaa-attttcatcca---gcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagct--ttccgttttatcag
|||||||||||||| |||||||||||||| ||||||||||||||||| ||||| ||||||| || || ||| |   || ||| |  |||||||       |||  |   | |||  |       | |    ||  |  |||   || |||||
GTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatattgatctaagtgctctgttggttaatgg-------aagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G28730.2 (Glycine max), 5'ss of exon 7
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaa-attttcatcca---gcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagct--ttccgttttatcag
|||||||| ||||| |||||||||||||| ||||||||||||||||| ||||| ||||||| || || ||| |   || ||| |  || ||||       |||  |   | |||  |       | |    ||  |  |||   || || ||
GTGAACCCGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatattgatctaagtgctctgttagttgatgg-------aagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 8
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatccagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttatcag
||||| |||||||| |||||||||||| ||||||||||||||||||| ||||| |||||||| |||    ||||  | | | ||| |||| |     |||  || |  | |||   | |||  ||    |  |   | |  | |||
GTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTGgtaaagttta--tcagctatagctcttagtggttt-----agttttcctagtccatgcttagattatgac--gtgtcatggtcca-cag

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 5'ss of exon 7
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatc-cagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttatcag
||||||||||||||||||||||| ||| | |||||||| |||||||| ||||| ||||||| ||||  |  ||   ||  | |  |||    || || ||| ||    | |  | | |   ||| |                     
GTGAACCCACACACGCATCAGCTAAAAATATGTGATTTCGGGAGTGCAAAAGTGTTGgtaagttttattgacacagcttttaacgaattcattcttggagt-atgacatgttctcgttctctgtag---------------------

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 5
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatccagc-actggttattaatggtgtcatgaagtcatcttgtttcattgc-----ttgatgtt--ggtcagctttccgttttatcag----
||||| || || ||||| ||||||||||| ||||||||||| |||||||||||  |||| | | |  |       | ||  ||||  | | ||   | ||||   ||    | | |      ||  ||||  ||  |    | ||||           
GTGAATCCTCATACGCACCAGCTGAAACTGTGTGATTTTGGAAGTGCGAAAGTGCTGgtgagtatctactggattagtgagtattt-tcgagttgcgcagtcgcattacagcgtcgaagcaatttgtgtttcggaaatgcgtgcgttgcggtgacagg

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 5
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatccagcactggttattaatggtgtcatgaagt-catcttgtttcattgcttgatgttggtcagctttccgttttatcag----------
||||| || || |||||||||||||| ||||| |||||||| || ||||||||| |||| |  | |     |  |  |    |   ||  ||  |    |   | ||   |   |   | |  || |  |       |||||   |           
GTGAATCCTCATACGCATCAGCTGAAGCTTTGCGATTTTGGTAGCGCGAAAGTTCTGgtgagatatgtgatataaacgagcgtggttgcagttttcccctgtgtattagatgggtcaataaaatttgaaaatgcaaggttttgaaaaaaaagagatc

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 6
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatccagcactggttattaatggtgt--------catgaagtcatcttgtttcattgcttgatgttgg---tcagctttccgttttatcag-
||||| || |||||||||||||| || || || || ||||| ||||||||||||||||| |  | | ||  |    | || |||  |||| |        ||  | |||||   ||| ||| |   |||    |   ||   ||    |||| |    
GTGAATCCCCACACGCATCAGCTAAAGCTATGCGACTTTGGAAGTGCGAAAGTTTTGgtgagatgtgatgaaatgtttgtgatttgtggttttttcctttcacaaggtcatgcagtt-catagagagatagaagggctccagttgagatttttttttt

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|46917752|gb|CN547081.1|CN547081
EST:     CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG                         GTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
genomic: CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttc ... gttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
EST: gi|30126156|gb|CB911495.1|CB911495
EST:     GAAACTTTGTGATTTTGGGAGTGCAAAAGTTTTG                         GTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
genomic: GAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttc ... gttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
EST: gi|110726124|gb|EE101641.1|EE101641
EST:     CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG                         GTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
genomic: CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttc ... gttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
EST: gi|161715603|gb|FC067769.1|FC067769
EST:     CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG                         GTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
genomic: CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttc ... gttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
EST: gi|156736132|gb|EV240253.1|EV240253
EST:     CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG                         GTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
genomic: CACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttc ... gttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
EST: gi|30130728|gb|CB916067.1|CB916067
EST:     GAAACTTTGTGATTTTGGGAGTGCAAAAGTTTTG                         GTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC
genomic: GAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttc ... gttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTGgtaaattttcatccagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttatcag

- - - - - - - -  TCAGCT
- - - - - - - - - CAGCTG
- - - - - - - - -  AGCTGA