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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcctttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa...

Basic information

species Vitis vinifera
transcript Vv11s0052g00880.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 5'ss of exon 11
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcctttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa
|||| || ||||| ||||| ||||||||||| ||||| ||||||||||| |||||||| ||  | ||||| ||||| || || || |||||||| || | || |    | ||   |||     | ||    | ||| ||     ||||     |  ||  | |  | ||      |     |  |||| | |        
TGGCAGAGTTCCCTTCAGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCCGTTGCTCCTCGTCTTCAGCCGAGATACTACTCAATTTCATCTTCACCTAGgtaaaatatccta--cttatgctttttcttcctcattttaaaattgtt-----ccttacctttttattgacatgcatttccttcttccatcag-------

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 11
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcctttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa
|||| || ||||| || || ||||||||||| ||||| ||||||||||| ||||| || ||  | || || ||||||||||| || |||||||| || | || | ||   |    | |  || | ||   || |||| |     | ||  |    ||    ||  ||| |  | | | || | ||   | |         
TGGCAGAGTTCCCTTCGGCAAAGCCTCCACTAGGAGTCTTCTTTGCAGCTGTTGCCCCTCGACTTCAACCAAGATATTATTCTATTTCATCTTCACCTAGgtaaatagccccactcat--aatttttccttctcatcatg--aatatttgttttcct----gttgact-tacatttc-ctttcatctggcag--------

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 12
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcct-ttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa-
|||||||||| ||||||||||| |||||| |||| || || ||||||||||||||||| ||| ||||||| |||| |||||| || || || || |||| || | | | | | |  |  |     ||||       |   | || | ||         |       |||| | || | ||||  |      || ||      
TGGCTGAATTTCCATCAGCCAAACCTCCAATTGGTGTCTTTTTTGCAGCAGTTGCTCCTCGCCTGCAGCCTAGATTTTATTCAATCTCCTCATCTCCAAGgttaatttctttttattgcttttgcattactgtttgtacatgtggtatttg-gttggcatgcagtgactggg-aagagactagtaaaaacgaagaccaagtt

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA17G07050.2 (Glycine max), 5'ss of exon 12
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcct-ttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa-
|||||||||| ||||||||||| |||||| |||| || || ||||||||||||||||| ||| ||||||| |||| |||||| || || || || |||| || | | | | | |  |  |     ||||       |   | || | ||  |      |  |    |||  | || | ||||  |      || ||      
TGGCTGAATTTCCATCAGCCAAACCTCCAATTGGTGTCTTTTTTGCAGCAGTTGCTCCTCGCCTGCAGCCTAGATTTTATTCGATCTCCTCATCTCCAAGgttaatttctttttattgcttttgcattactgtttgtgcatgtggtattg-tgtgggcatgtagtgact-cggaagagactagtaaaaacgaagaccaagtt

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 5'ss of exon 12
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcctttcaaatattagatcgcatctttttgctgttaatacctctag-atgtcaactgtgtaatacactatgattccgtaaaactgtaa--
|||| || || || ||||||||||| |||||||| || ||||| || | |||||||||| | |||||||| || |  ||||| |||||||| || || |||||||||  |   |  | |      ||   ||      || | |  || | || | ||   |||     ||||| |   | ||  | ||||  |  ||||   
TGGCCGAGTTTCCTTCAGCCAAGCCACCACTTGGTGTCTTCTTCGCTGGAGTTGCTCCAAGGTTGCAGCCTAGGTTCTATTCGATATCATCATCGCCCAAgtgagtaccttcattgtcttggtctttttgtcttcaagttgttcgcttgagacttatattgtgtttttagtgtattgagc-attgtcccgtttacttgtatag

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|110695029|gb|EE072582.1|EE072582
EST:     GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCCTCCCCAAA                         GATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
genomic: GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtattt ... acttttacagGATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
EST: gi|27582064|gb|CB004759.1|CB004759
EST:     GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCCTCCCCAAA                         GATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
genomic: GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtattt ... acttttacagGATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
EST: gi|30300181|gb|CB976975.1|CB976975
EST:     GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAA                         GATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
genomic: GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtattt ... acttttacagGATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
EST: gi|110699884|gb|EE077290.1|EE077290
EST:     GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAA                         GATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
genomic: GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtattt ... acttttacagGATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
EST: gi|71864604|gb|DT013659.1|DT013659
EST:     GTTGCTCCACGCTTACAGCCCAGATATTATTCCATATCATCCTCCCCAAA                         GATGGTGCCATCTAGAATTCATGTCACTTGCGCCTTGGTTTGTGATAAGAT
genomic: GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtattt ... acttttacagGATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
EST: gi|32270293|gb|CD719452.1|CD719452
EST:     GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCCTCCCCAAA                         GATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT
genomic: GTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtattt ... acttttacagGATGGTGCCATCTAGAATTCATGTCACTTGTGCCTTGGTTTGTGATAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAGCAGTTGCTCCACGCTTGCAGCCCAGATATTATTCCATATCATCTTCCCCAAAgtgagtatttctgtcctttcaaatattagatcgcatctttttgctgttaatacctctagatgtcaactgtgtaatacactatgattccgtaaaactgtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaaac