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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctctctcatttttccttgcgataatgtgatgaagcacatggctagtgtgcaaaagtattctcttttctgcattatctct...

Basic information

species Vitis vinifera
transcript Vv07s0129g00270.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 3
AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctctctcatttttccttgcgataatgtgatgaagcacatggctagtgtgcaaaagtattctcttttctgcattatctct--
|||||| ||||||||||| || ||||| ||||||||||||||||| ||||| ||  | |||||||| || || |||||||| || ||||||||||| |||| ||| | | |  |||| | | | |   | |         ||   |   |  |   | || | |  | |||       || |  |||   | |||  |    
AAGTCTTATATTTGAATATGTCAATAACACTGATTTTAAAGTGCTCTATCCTACATTGTCAGACTACGAAATACGATATTATATTTATGAACTTCTGAAGgcaagttttatg-ctctat-tgtttaataataaagaacatgaactttccacaactaatatagtttttttgcttttacttttttgtttaatccttacattgtg

upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 3
AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctctctcatttttccttgcgataatgtgatgaagc--acatggctagtg--tgcaaaagtattctcttttctgcattatctct
|||||| ||||||||||| || ||||| ||||||||||||||||| ||||| ||  | |||||||| || || |||||||| || | ||||||||| |||| ||| ||| | ||||| |   | | | ||  |    | |   ||  ||    | |  | || | |  ||  |  |  | | || |  |     |||  | |  
AAGTCTTATATTTGAATATGTCAATAACACTGATTTTAAAGTGCTCTATCCTACATTGTCAGACTACGACATACGATATTATATTTTTGAACTTCTGAAGgcaagttctat-tctctat---tgtttaataatgaagtacatgaacttggcacaactgatattgtttttgcttttactatttttttaatcctcacatcgtgttg

upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G23070.1 (Arabidopsis thaliana), 5'ss of exon 3
AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctct----ctcatttttccttgcgataatgtgatgaagcacatggctagtgtgcaaaagtattctc--ttttctgcattatctct
 ||  | ||||||||| | ||||| ||||  ||||| ||||| || |||||||||||||||||||||||| ||||||||||||| | |||||||||||||||||    ||  | ||      | |    |    ||||| |||||    | ||   |    ||    || |  | | |  |||  |   | |   || | ||    
CAGCTTGATATTTGAACATGTGAACAATAAAGATTTCAAAGTTCTCTATCCAACTCTCTCAGACTATGATGTTCGATATTACATTTTTGAACTTCTAAAGgtaattattcagtttcctgaattgtagaccatgattttctttgcggc--tttggcaattggcaaaagtaatcggtagatatatcatagatgtatagcgtcat----

upper sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 4
AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctctctcatttttccttgcgataatgtgatgaagcacatggctagtgtgcaaaagtattctcttttctgcattatctct---
 || ||||| ||||| || ||||| ||||||||||| |||||||| || || |||||  |||||| |||||| ||||| |||||  |||| || || ||||| ||   ||  ||| | |  |         | | |||  | |  |||   ||| ||    |||  | ||| |  || |          |     | |     
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttttccgaggcttgatctgctt--ggttttgtacagaaacatgatgctgat-tgcgaccgtgtatcgcccaaagtgacgtttagacc

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|77589565|gb|DV224064.1|DV224064
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|110362193|gb|EC925709.1|EC925709
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|71883675|gb|DT032730.1|DT032730
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|27586807|gb|CB009502.1|CB009502
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|110396473|gb|EC962161.1|EC962161
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|71883451|gb|DT032506.1|DT032506
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|161717971|gb|FC069266.1|FC069266
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|33402558|gb|CF208185.1|CF208185
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|110717101|gb|EE092665.1|EE092665
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
EST: gi|110703175|gb|EE079801.1|EE079801
EST:     CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAG                         GCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA
genomic: CAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctc ... atatatgcagGCATTAGATTACTGCCACTCACAGGGTATCATGCATCGAGATGTAAAGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctctctcatttttccttgcgataatgtgatgaagcacatggctagtgtgcaaaagtattctcttttctgcattatctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctc
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