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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatgttaaataatgttaaattacttgaggatcgctgttatcattattgtttctacattctgctttatactcgatatgatttgtagatcat...

Basic information

species Vitis vinifera
transcript Vv10s0003g04390.t01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: LOC_Os04g52900.2 (Oryza sativa), 5'ss of exon 19
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatgttaa-ataatgttaaattacttgaggatcgctgttatcattattgtttctacattctgctttatactcgata-tgatttgtagatcat
||| ||  |||| || ||||| || || || |||||  |||||||||| |||||||||||||| ||  | |||||  ||||||| ||||| |||||||||||   |   || || ||  |    | |  ||   || |   |  | ||   |       | || |   |     |   | | | || || | |  |  |   
AAAACAGAGAGTCTCAATGGCAAGAGCTGTTTATTCTGATTCAGATGTCTACATATTTGATGATCCACTGAGTGCATTAGATGCCCATGTTGGTCGACAGgtgcattcatcttgctaccactgcggttcatgctttcaattttacagtctcccccgcattatcaaatctgccagtggcagttggtaatggtgtcaatgtt--

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM2G084181_T01 (Zea mays), 5'ss of exon 19
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatgttaaataatgttaaattacttgaggatcgctgttat-cattattgtttctacattctgctttatactcgatatgatttgtagatcat
 |||||| ||||||| ||||| || || || |||||  ||||||||||||||||||||||||| ||  | |||||  ||||||| ||||| || || ||||| | |    ||| ||   |   |||    |  ||  |        | |   | |        |  |   |  || | |  | || | ||| |   | | |
GAAGCAAAGAGTTTCAATGGCAAGAGCTGTGTATTCTGATTCAGATGTGTACATATTTGATGATCCACTCAGTGCATTAGATGCCCATGTTGGCCGGCAGgtgaattcaccatcttgcttgtggtttctatttttatgatctatactcacatactgaaaaggatgaaccatcgttcagatcc-atgttattaggttacctt

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA13G29180.1 (Glycine max), 5'ss of exon 19
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatgttaaataatgttaaattacttgaggatcgctgttatcattattgtttctacattctgcttta--tactcgatatgatt-tgtagatcat
||||||  |||| ||||||||||| || || || || ||||| ||||||||||| |||||||||||  |||||||||| ||||| ||||||| | ||||||| |    ||||||  || | |        ||     ||    ||||| |   ||||| |||    |||    | |  || |  ||   ||  | | |||  |
AAAGCAGAGAGTATCCATGGCTAGAGCTGTCTACTCAAATTCTGATGTGTACATCTTTGATGACCCCCTAAGTGCTCTGGATGCACATGTGGCTAGACAGgttacc--ttcatgccaattgactcctctataga-atggcctactgttgtttctattgcttcagtgttcaaactcaagtaatttatgctatggtattgattgt

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA15G09900.1 (Glycine max), 5'ss of exon 19
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatgttaaataatgttaaattacttgaggatcgctgttatcattattgtttctacattctgctttatactcgatatgatttgtagatcat----------
||||||  |||| ||||||||||| || || || |||||||| ||||||||||| |||||||| ||  |||||||||| ||||| ||||||| | ||||||| |    ||||||  || | |        | ||  |      |||||||   ||||| |||    ||||   | | |    || || | ||   ||  |          
AAAGCAGAGAGTATCCATGGCTAGAGCTGTCTACTCCAATTCTGATGTGTACATCTTTGATGATCCCCTAAGTGCTCTGGATGCGCATGTGGCTAGACAGgttacc--ttcatgccaactgac-------tcctctatagcttctgttatttctattgcttcagtgttctaactcaaaagtaatttgctatg-gcattgtttttggtcat

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT2G34660.2 (Arabidopsis thaliana), 5'ss of exon 20
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatg------ttaaataatgttaaattacttgaggatcgctgttatc----attattgtttcta--cattctgctt-tatactcgatatgatttgtag-atcat--------
 |||||  | ||||||||||||||||| || || || ||||||||||||||||| ||||||||||| |||||||| || ||||||||||| |||| ||||||| | | |   ||      ||  |||| | ||   || || |   | |   |||||    ||| |||| |||   |||| ||    ||   ||  | |||||| ||| |  ||        
GAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATGTGTACATCTTTGATGACCCGTTAAGTGCCCTTGATGCTCATGTTGGTCAACAGgtactaactcattgattctctttgataaggctagtctatttcatttttgaatttatctaacatttttgtgtctggtcattatgggaatactgtcagtctgatttctaggaatattgtttcag

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT1G30400.1 (Arabidopsis thaliana), 5'ss of exon 20
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaa------------ttatttcatgttaaataatgttaaattacttgaggatcgctgtta-tcattattgtttctacattctgctttatactcgatatgatt--tgtagatcat-------------------------------------------------------------------------------
||||||  | ||||| ||||||||||| || || || |||||||| |||| ||| || |||||||| || ||||| || ||||| ||||| ||||  |||||||             | |||    |  || |||  |   ||  |     |    ||  | || | |    |   || || || |||  | ||   |||  |  | ||  || |                                                                               
AAAGCAGAGGGTTTCTATGGCTAGGGCCGTTTACTCAAATTCAGACGTGTGCATCTTAGATGACCCATTGAGTGCCCTTGATGCGCATGTTGGTCAGCAGgtaaactagccataggctcttttggatagaacaatactttgtttttctttcaattttgcaaatcgtgaactctataacgttttgtttttcaatctgcatggatattctacttcttgtttgccacggatctctgccatatactacttttaagcaaacattgttatctgatgttcgaaactggctgttatatatag

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|30304105|gb|CB980899.1|CB980899
EST:     ACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAG                         GTTTTTGATAGATGCATCAAGGGAGAATTAAGAGGGAAAACCAGAGTTCTC
genomic: ACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattattt ... tcatttccagGTTTTTGATAGATGCATCAAGGGAGAATTAAGAGGGAAAACCAGAGTTCTC
EST: gi|30304042|gb|CB980836.1|CB980836
EST:     ACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAG                         GTTTTTGATAGATGCATCAAGGGAGAATTAAGAGGGAAAACCAGAGTTCTC
genomic: ACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattattt ... tcatttccagGTTTTTGATAGATGCATCAAGGGAGAATTAAGAGGGAAAACCAGAGTTCTC
EST: gi|34549912|gb|CF518144.1|CF518144
EST:     ACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAG                         GTTTTTGATAGATGCATCAAGGGAGAATTAAGAGGGAAAACCAGAGTTCTC
genomic: ACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattattt ... tcatttccagGTTTTTGATAGATGCATCAAGGGAGAATTAAGAGGGAAAACCAGAGTTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATGTGTACATATTTGATGACCCTTTAAGTGCTCTAGATGCTCATGTGGGTCGACAGgtaattatttcatgttaaataatgttaaattacttgaggatcgctgttatcattattgtttctacattctgctttatactcgatatgatttgtagatcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaataa