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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCAGACGTTCTTGATTCTGCATTGCTAAGGCCTGGGAGGTTCGATCGACAGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttattcacaaaccctgcttattgcttattcatttgctgcttgtggttggtgtcgtcacacagattttagaatcaaaatgcgctgtatggaaatt...

Basic information

species Vitis vinifera
transcript Vv18s0001g00190.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA06G02200.1 (Glycine max), 5'ss of exon 1
ACCAGACGTTCTTGATTCTGCATTGCTAAGGCCTGGGAGGTTCGATCGACAGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttattcacaaaccctgcttattgc--ttattcatttgctgcttgtggttggtgtcgtcacacagattttagaatcaaaatgcgctgtatggaaatt
||| || ||||||||||| || ||| | ||||||||  |||||||| | || |||||||||||||| ||||||||||| || |||||||| ||||||||||| ||| | |   ||  |    | ||      | |  | |||| |  ||||  ||| | |      || | |  ||| || | |||      |    ||  |
ACCGGATGTTCTTGATTCGGCGTTGTTGAGGCCTGGCCGGTTCGATAGGCAAGTTACTGTGGATAGACCTGATGTTGCCGGCAGAGTTAAAATCCTTCAGgtgagtctgtct-cagccataacataacatcataacccttttgata-ttgttattgttctttaattactgttactagtattagaatttcacttccataacct

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA04G02100.1 (Glycine max), 5'ss of exon 1
ACCAGACGTTCTTGATTCTGCATTGCTAAGGCCTGGGAGGTTCGATCGACAGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttattcacaaaccctgcttattgcttattcatttgctgcttgtggttggtgtc-gtcacacagattttagaatcaaaatgcgctgtatggaaatt-
||| || ||||||||||| || ||| | ||||||||  |||||||  | || |||||||||||||| ||||||||||| || |||||||| || |||||||| |  | |  || || || |    | |  ||||| | || ||  | |   ||    ||  | ||| |  |     || |   ||    |  |  | | |  
ACCGGATGTTCTTGATTCGGCGTTGTTGAGGCCTGGCCGGTTCGACAGGCAAGTTACTGTGGATAGACCTGATGTTGCCGGCAGAGTTAAAATTCTTCAGgtgacataa--cataacccttttcaaattgttatttaattactattagaatttcccttccataacatacctaacctaacctttattaagtagagaggagtgc

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 5'ss of exon 1
ACCAGACGTTCTTGATTCTGCATTGCTAAGGCCTGGGAGGTTCGATCGACAGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttattcacaaaccctgcttattgcttattcatttgctgcttgtggttggtgt-cgtcacacagattttagaatcaaaatgcgctgtatggaaatt
 || |||||||||||||| || ||| | |||||||| ||||| ||||||||||| || ||||||||||||||||| ||||| ||||| ||||| |||||||||    | |||| |     |   ||  | ||| |  ||||    | | | |  |||   |   |  |  | |    ||     |  | | |||   |   
GCCGGACGTTCTTGATTCGGCTTTGTTGAGGCCTGGAAGGTTTGATCGACAGGTCACGGTGGATAGGCCTGATGTGGCTGGCAGAGTCAAGATTCTTCAGgtt---cttttcatagctgttttataaaggttactggtttgtctatggagttatgtgaatgattcttatttctctctatggggtttggttttattttag--

upper sequence: Vv18s0001g00190.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 5'ss of exon 1
ACCAGACGTTCTTGATTCTGCATTGCTAAGGCCTGGGAGGTTCGATCGACAGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttattcacaaaccctgcttattgcttattcatttgctgct-tgtggttggtgtcgtcacacagattttagaatcaaaatgcgctgtatggaaatt
||| || |||||||| || || ||||| || ||||| || || || || || || || ||||||||||||||||| || || |||||| |||||||| |||||  ||  | |    |   |   |     | |  || | |   |  ||||||   |   ||      | || | | |                       
ACCGGATGTTCTTGACTCCGCGTTGCTGAGACCTGGTAGATTTGACCGGCAAGTCACAGTGGATAGGCCTGATGTAGCCGGAAGAGTTCAGATCCTTAAGgtttcttcttgctttcattttctgttagagtgaaacaatggagacagtgtggtgaataatgttgtgtggtttattgcag----------------------

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|110713388|gb|EE089264.1|EE089264
EST:     AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAA                         GTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTNGAAA-GAT
genomic: AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttat ... tgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTT-GAAAAGAT
EST: gi|110383931|gb|EC948337.1|EC948337
EST:     AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAG                         GTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
genomic: AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttat ... tgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
EST: gi|352790761|gb|FQ478309.1|FQ478309
EST:     AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAG                         GTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
genomic: AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttat ... tgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
EST: gi|352794299|gb|FQ481530.1|FQ481530
EST:     AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAG                         GTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
genomic: AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttat ... tgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
EST: gi|352798544|gb|FQ480569.1|FQ480569
EST:     AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAG                         GTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
genomic: AGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttat ... tgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
EST: gi|110377726|gb|EC942808.1|EC942808
EST:     GCTGGTAGAGTTAAGATCCTTCAG                         GTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT
genomic: GCTGGTAGAGTTAAGATCCTTCAGgttagtttat ... tgtatgacagGTGCACTCAAGAGGGAAGGCACTAGCCAAGGATGTAGACTTTGAAAAGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAGACGTTCTTGATTCTGCATTGCTAAGGCCTGGGAGGTTCGATCGACAGGTTACTGTGGATAGGCCTGATGTTGCTGGTAGAGTTAAGATCCTTCAGgttagtttattcacaaaccctgcttattgcttattcatttgctgcttgtggttggtgtcgtcacacagattttagaatcaaaatgcgctgtatggaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggaaa