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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggatctctacatacttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa...

Basic information

species Vitis vinifera
transcript Vv01s0150g00090.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 5'ss of exon 14
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggatctctacatacttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa----
 ||||| ||||| || ||||||||||| ||  ||||||||||||| ||||| || || ||||| || |||||| | |||||||| |||||||| ||||||||||||   |     |   ||     |      ||||  ||  |    | || |     |   |||  ||  ||| |  |   |  |  |  ||   |      
AGCTCTTATTGCTCACTTCCAGAACTCCAGTTTGATGAATGAGGACAAGCGCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctttctctctctctctctctctctctctctc-tctctctctcgttgat---aaatggagttaaagcagcagatgacacttggacacagtttgctgtt

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G451716_T01 (Zea mays), 5'ss of exon 14
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatga---ggatctctacat-acttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa
 |||||  |||| |||||||||||||||||  |||||||||||||||| || || || || || ||||||||  |||||||||| |||||||| ||||| |||||      |  | | ||| |||    ||       |  |    | ||||    ||  |||  |  || |  ||| |||   ||  | | |  |||      
AGCTCTAGTTGCTCATTTCCAGAACTCAAGTTTGATGAATGAGGATAAACGCTGCCGCCCTATACTCTTCCACTCTGATGGTCCGAATGCAGGAGATCAAgtatgctctctacttgtccatcactctctattatctgttgcatcatggtatatgactatatggtgactagtagttcctgaactctgctgcttatcgcata----

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G459746_T01 (Zea mays), 5'ss of exon 14
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggatctctacatacttcacatagaggactctaatcagttatacatttacctgg--acaagaggaaatccagaaacttgaagataaaggcaacctaa
 ||||| ||||| |||||||||||||| ||  ||||||||||||| || || || || ||||| ||||||||  | |||||||| |||||||| |||||||||||   || |||   |  ||        ||    |   | | |||    ||  |  |  |||  | |     | | |       |  |   |    ||  
AGCTCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGTTGCCGCCCCATACTCTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttatttcttttttattttgtcgttggtactttccctgctatcttgttctccagttacattatgtttcgctgcagtgcactgtgacgagtcttct--

upper sequence: Vv01s0150g00090.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM5G814700_T01 (Zea mays), 5'ss of exon 4
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggatctctacatacttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa----
 || || ||||| |||||||||||||| ||  ||||||||||||| || || || || ||||| || |||||  | |||||||| |||||||| |||||||||||   || |     || ||      | | ||| |   |   | |   |||  | ||  |         |      ||||    |   | |||         
AGCCCTGATTGCTCATTTCCAGAACTCTAGTTTGATGAATGAGGACAAACGCTGCCGCCCCATACTTTTCCACTCAGATGGTCCTAATGCAGGAGATCAGgtatgcttatttt---gtattttgtcctgggtactttc-cctcctgtctttttctccggttacattatgtactgttgtcttgtgagttgtgacaagtcttctct

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|83274793|gb|DV938889.1|DV938889
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATACAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|46910430|gb|CN545805.1|CN545805
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|32245817|gb|CD711636.1|CD711636
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|110732197|gb|EE107275.1|EE107275
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|110429936|gb|EC996451.1|EC996451
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|110379026|gb|EC944195.1|EC944195
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|110389267|gb|EC954091.1|EC954091
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
EST: gi|32245389|gb|CD711208.1|CD711208
EST:     GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAG                         GTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA
genomic: GATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggat ... ttctcggcagGTGCCTTTCCCAATGGGAGTAAATGTTCGATCTAGACCTGGAAAAACTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCTCATTGCCCATTTCCAGAACTCAAGCCTGATGAATGAGGATAAGCGATGTCGTCCCATTCTCTTCCATACTGATGGTCCCAATGCAGGTGATCAGgtatgaggatctctacatacttcacatagaggactctaatcagttatacatttacctggacaagaggaaatccagaaacttgaagataaaggcaacctaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggcaa