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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcgttggatctgaaatttagggttcgaagatttcttttagttttgattctgtgtttggttgctgaaacaatacagttttagaaaaaaaaaaaa...

Basic information

species Vitis vinifera
transcript Vv06s0061g00810.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G08760.1 (Glycine max), 5'ss of exon 3
GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtg-------tcgttggatctgaaatttagggttcgaagatttctt-ttagttttgattctgtgtttggttgctgaaacaata--cagttttagaaaaaaaaaaaa
 ||||||||||||||||||||||| || |||||||| |  |||||||| |||||||| ||||| |||        || ||       |  |||  | ||||    |   |  | ||| ||  |  | | |||| ||  ||||  || |    ||||||             
ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtagtaacactctttctccacaatttttgtgcttcgtgcgtgattgataagtgtttgtgatttttttgttttttgaattaaaaactcgttttatgc----------

upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G19780.1 (Glycine max), 5'ss of exon 3
GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg----ttggatctgaaatttagggttcgaagatttctttta---gttttgattctgtgtttggttgctgaaacaatacagttttagaaaaaaaaaaaa
 ||||||||||||||||||||||| || |||||||| |  |||||||| |||||||| ||||| ||| |      ||    || |  |||  |  | |    |   | |||   ||||    | | | |||  ||  | ||| ||  |  |||||   | ||      
ACATGTGGTTCTTCCTCCTGAAGTCGCAAAACTGCTTCCCAAGAATCGTCTTCTCTCCGAAgtaagtattcactttttcccctcagttttgtgccttgtgcgtaattgttaagcgtttgtggtttttttttatttatttaaa-aactcgtttttatgtagaa------

upper sequence: Vv06s0061g00810.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G08890.1 (Glycine max), 5'ss of exon 2
GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcgttggatctgaaatttagggttcgaagatttcttttagttttgattctgtgtttggttgctgaaacaatacagttttagaaaaaaaaaaaa-------
 || |||||||| ||||||||||| ||||||||||| |  |||||||| |||||||| ||||| |||    ||   | || ||  ||   || |||    | ||  | | ||| |    | | |   |    ||| |||| ||||||||     | |           
ACACGTGGTTCTGCCTCCTGAAGTTGCCAAACTGCTTCCTAAGAATCGACTTCTCTCCGAAgtaagtac--ttatttttgtaaaatatattttgaaa---ttttaaaatattggtctaatttata--taaaaaaataatatagttttagttcctatattttactaaaa

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|110397972|gb|EC964000.1|EC964000
EST:     TTCCTCCTGAAGTGGCGAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110392141|gb|EC957352.1|EC957352
EST:     TTCCTCCTGAAGTGGCGAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|71871580|gb|DT020635.1|DT020635
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|26257279|gb|CA808342.1|CA808342
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110408895|gb|EC974543.1|EC974543
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110383778|gb|EC948178.1|EC948178
EST:     TTCCTCCTGAAGTGGCGAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|26262419|gb|CA813482.1|CA813482
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTT-AGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110423493|gb|EC989839.1|EC989839
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110401256|gb|EC967859.1|EC967859
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110423682|gb|EC990033.1|EC990033
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|71868904|gb|DT017959.1|DT017959
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110423336|gb|EC989681.1|EC989681
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|26257549|gb|CA808612.1|CA808612
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110414078|gb|EC979902.1|EC979902
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
EST: gi|110396029|gb|EC961703.1|EC961703
EST:     TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAA                         AATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT
genomic: TTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcg ... ttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTAT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATGTGGTTCTTCCTCCTGAAGTGGCCAAACTGCTCCAGAAGAATCGGCTTCTCTCGGAAgtgagtgtcgttggatctgaaatttagggttcgaagatttcttttagttttgattctgtgtttggttgctgaaacaatacagttttagaaaaaaaaaaaa

- - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa