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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattcttggtgcatcttatttcaattctctattgagggttgggttaattgatgtggtttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA

Basic information

species Vitis vinifera
transcript Vv05s0051g00340.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 3
--ttgattcttggtgcatcttatttcaattctctattgagggttgggttaattgatgtggtttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
     | | || ||    | ||   |  || | | ||     || |    | || |||| | | |  ||   | |    | | | ||| |   | | | ||||| || || |||||  | ||||| || | |||| | || ||||| ||||| || ||||| |||||||| || |||||||||||||||||| || ||||||
agcacagtgtttgttgggcctacaact-ttttatgtttttattttgtcagagtgctgtgttgtgttatttgcagattggacttaacgtgtctat-tatgcagGGACGCAATGTGGTTATTGAGCAGAGCTATGGTTCACCGAAAGTCACAAAGGACGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGA

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------ttgatt---cttggtgcatcttatttcaattctctattgagggttgggttaatt--gatgtggtttatacttaaaaaaggttaatcagcgttttgttgtttcc--agGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
                                        |||||   |  |  |   |||  ||    | |   ||| | |   |||| |||  |    |  ||     ||| |     |  |    ||  |  |  ||    |||| ||||| || ||  | ||||||||||  ||||| || |||||||||||||||||||| |||||||| ||||| ||||||||||| ||   ||| ||||
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------ttgattcttggtgcatcttatttcaattctctattgagggttgg--gttaattgatgtggt----ttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
                                                         |  ||     |  ||    |  | |     |    ||  |      |    || | || |    | | |||     |   |  ||           | |||  |||| ||||| ||  |  | || ||||| |  ||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||||||| |||| ||||
gtataaacttatgtttcagataatttctgtgtaagagacttgtattgtaagtgaatctagttaaaaatagataacgtgacgacctattgacaagtatcaacaatcgtctgttttgttaccctcacactctctgatactacatgtctaaaaccatttttgaagGGTCGTAATGTCATCATCGAACAAAGCTGGGGTGCACCAAAGGTGACAAAGGATGGTGTGACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGA

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------ttgattcttggtgc---atcttatttcaattctctattgagggtt-----gggttaattgatgtggtttat-acttaaaaaaggttaatcagcgttttgttgtttc-----cagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
                                                                    |   | | | | |   || ||| ||  | |     | |  | ||     || ||   | |  | |||||  | ||||      |       |||| || | | |      ||||| || |  ||  |  | ||||||  ||||||  | || |||||||| || |||||||| |||||||| ||||||||||| ||||||||  |  | ||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGA

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|161718112|gb|FC066924.1|FC066924
EST:     AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAG                         GGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
genomic: AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAGgtaaacttct ... ttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
EST: gi|30300026|gb|CB976820.1|CB976820
EST:     GAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAG                         GGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
genomic: GAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAGgtaaacttct ... ttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
EST: gi|110690897|gb|EE068383.1|EE068383
EST:     AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAG                         GGTCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
genomic: AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAGgtaaacttct ... ttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
EST: gi|71859154|gb|DT008209.1|DT008209
EST:     AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAG                         GGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
genomic: AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAGgtaaacttct ... ttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
EST: gi|110731644|gb|EE106246.1|EE106246
EST:     AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAG                         GGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
genomic: AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAGgtaaacttct ... ttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
EST: gi|71859121|gb|DT008176.1|DT008176
EST:     AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAG                         GGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA
genomic: AGGGCGTGGAAGAGCTCGCAGATGCTGTTAGAGTCACCATGGGCCCCAAGgtaaacttct ... ttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattgatgtggtttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA
                            ggttaat  putative branch site (score: 4)
                                             ttgtttcc  putative PPT
             tttatacttaaaaaag  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattcttggtgcatcttatttcaattctctattgagggttgggttaattgatgtggtttatacttaaaaaaggttaatcagcgttttgttgtttccagGGGCGTAACGTGGTACTAGAGCAAAGTTTTGGTGCCCCAAAAGTGACAAAAGATGGTGTAACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGA

- - ttcttgg
- - - - - -tgcatct
- - - - - - - - - - - - - - - - - - - ggttggg
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa