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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattgtaagtcttatttgtagttagtttttgtgcacaacatattagctgtcaattttaatcaccaaatgttgagtcttacaaaatctgcctgatt...

Basic information

species Vitis vinifera
transcript Vv02s0012g01850.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G13410.1 (Glycine max), 5'ss of exon 3
TTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattgtaagtcttatttg---tagttagtttttgtgcacaacatattagctgtcaattttaatcaccaaatgttgagtcttacaaaatctgcctgatt----
|||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||| || || |||||||||||||| ||  |||| |||||||| |||| ||| |   || | ||||| |     || |   |||  |  |||     |   | ||    ||  |    || |||   |  ||      ||||    ||     
TTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAGCGTACACTCCTTTTGTTCCTCAAGCAGTCCTTCCTTCGAGgtgatt-tgccaattattattagagcctgtaaaagtttaggggcaatcctgtgtttctc---ctttgtttttaagtgtgtggctttgtt---tctggacaataaaga

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G08200.1 (Glycine max), 5'ss of exon 3
TTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattgtaagtcttatttgtagttagtttttgtgcacaacatattagctgtcaat-tttaatcaccaaatgttgagtcttacaaaatctgcctgatt---
|||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||| || || |||||||||||||| ||  |||| |||||||| |||| |||  ||||  | ||||| | ||   ||    ||  |    | ||    |||   | |||  |    || |||   |  |       | ||    ||    
TTCAGGCAGTGTTGAAAGAGTTTCAGAAGGCACAACGTCTTGCAGCTGAGAGGGAAACAGCGTACACTCCTTTTGTTCCACAAGCAGTCCTTCCTTCGAGgtgatttatgtat-tattattag-agcctgtaaaagtttaggggaaatcctgtgtttctcttttgtttttaagtgtgtggcttcgttt--tttgaacaatgaag

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G33950.1 (Glycine max), 5'ss of exon 3
TTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattgtaagtcttatttgta-gttagtttttgtgcacaacatattagctgtc-aattttaat-caccaaatgttgagtcttac-aaaatctgcctgatt
|||| || || || ||||| |||||||||||||| || ||  |||| || |||||||| || || |||||||||||||| ||   || |||||| ||||||| || ||   || | ||||| |   |||||| | |||  | || |||||     |   |||||| | |||||||| ||     | |  | ||| |   | |  
TTCAGGCGGTGTTGAAAGAATTTCAGAAGGCTCAGCGTCTTTCAGCTGAGAGGGAAACAGCTTACACTCCTTTTGTTCCACAAGGAGCTCTTCCATCCAGgtgataata--aactgttattggagtgttagtatctgtcaataa-atattgttgatttgattttattgcaccaaatattcttattgattagaatttagattaa-

upper sequence: Vv02s0012g01850.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G46860.1 (Arabidopsis thaliana), 5'ss of exon 3
TTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattgtaagtc-ttatttgtagt----tagtttttgtgcacaa---catattagc----tgtcaattttaatcaccaaatgttgagtcttacaaaatctgcctgatt---------------------------------------------
||||||| |||||||||||||||||||| |||||||     || || ||||| |||||  | ||||||||||| || || || || | |||||| || ||||||      | | |  |||| ||| ||    |   | ||  || | |   |  |||||     ||   ||  ||| ||  ||   |    |  |  |   | ||  || ||                                             
TTCAAGCTGTTTTAAAAGAGTTTCAGAAAGCTCAACAAACTGCTGCTGAAAGAGAAACCACTTATACTCCTTTCGTGCCTCAATCTGCTCTTCCCTCTAGgtaacgtgactgattgattatatgtggtttcatgtatgttaagctcgaattcgaattagaagtgtgattatcataagcaaaaagcatcactttgtgaattgtttgtgtggttttgataatcatgttccttatttttcttgtctgactccgtatatag

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|349814626|gb|FQ399266.1|FQ399266
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|349814672|gb|FQ400310.1|FQ400310
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTCCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|349807660|gb|FQ402051.1|FQ402051
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|110690731|gb|EE068149.1|EE068149
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|349828272|gb|FQ416225.1|FQ416225
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|349823620|gb|FQ415030.1|FQ415030
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|349821234|gb|FQ404366.1|FQ404366
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|351021992|gb|FQ437779.1|FQ437779
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAGCG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
EST: gi|349817337|gb|FQ405341.1|FQ405341
EST:     AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAG                         CTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG
genomic: AGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattg ... tgatctgcagCTATACGGCAAGTGAGATAGATGTAGGTCCAGATAAGAGTCCTGAACAACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAAGCAGTTTTAAAAGAGTTTCAGAAGGCTCAACGGCTGGCAGCAGAAAGGGAAACGGCATATACTCCTTTTGTTCCCCAGTCAGTTCTTCCTTCCAGgtaattattgtaagtcttatttgtagttagtttttgtgcacaacatattagctgtcaattttaatcaccaaatgttgagtcttacaaaatctgcctgatt

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