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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactctttccatggggaattgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA

Basic information

species Vitis vinifera
transcript Vv05s0051g00340.t01
intron # 6
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 6
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 4
ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactctttccatggggaattg--ttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA
                | | |  |      | |  |   |  || ||    || || ||||  | | |  |  || |||  |   ||   | ||  ||||||||||| |||||||||| ||| || ||||||||||| |||||||||||  |||| |||||||| |  || || || ||||| || || || ||||||||||
---------------gtaagtaaatcgccgaatgattgctcatgttgctacttatatattggtcaaaacat--aattctgacgtgggtataatgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTGGACAGAGGTTATACTTCACCATACTTTATCACTAATCAAAAAACCCAAA

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactctttccatggggaattgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA
                | | || ||| ||||| | || ||   |   |||| |||   ||   |  || |  | ||   |   ||      ||| | |||||||| ||||| |||| ||||||  |||||||||||||||| |||||| | || || || ||||| ||||| || || ||||| |||| |||||| ||||
---------------gtgagttgaat-tttatccctaaat---gtcaaattattttgcttattccttaagg-tgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA

upper sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------------------------------------ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactcttt-----ccatggggaa----------ttgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA
                                                                            |        ||  | || || | ||| |||   |    |||  |   |   | || ||| |    || | || || ||  |       |  |||||          ||  || ||||||| || || ||||  ||||||||||| ||||||||||| |||||||| || ||||| || || |||||||| || || || ||   ||| || || |
gtaagtagatgtctgtgtgtcatactctcttgttttaccattgcggatttagttatggtttgcttcccgtgataggtacaagacgatgctgttgatgtcaatttttgacccgcgattgggagtagcgtatttaatagtggcatttttccaattcaatgatagtgactgggaaggggcggcgttttctgtagGATGGAAAAACTTTGTTCAATGAATTGGAGGTTGTTGAGGGTATGAAGCTCGACAGAGGATATATTTCCCCTTACTTCATTACCAATGCGAAGACACAGA

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:     CGCAAAGGCTATGGAGAAAGTTTGGCAA-GAGGGAGTAATCACA-TTTCA                         GATGGGAAGACATTGTATA-TGAATTGGAA
genomic: CGCAAAGGCTATGGAGAAAGTT-GGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAA
EST: gi|110686767|gb|EE064783.1|EE064783
EST:     TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
genomic: TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
EST: gi|30300026|gb|CB976820.1|CB976820
EST:     TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
genomic: TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
EST: gi|110691710|gb|EE070124.1|EE070124
EST:     TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
genomic: TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
EST: gi|110690897|gb|EE068383.1|EE068383
EST:     TTGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
genomic: TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
EST: gi|71873742|gb|DT022797.1|DT022797
EST:     TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
genomic: TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
EST: gi|77586617|gb|DV222437.1|DV222437
EST:     GCAAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
genomic: GCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTG
EST: gi|110731644|gb|EE106246.1|EE106246
EST:     TCGCAAAGGCTATGGAGAAAGTTGGCNAAGAGGGAGTAATCACAATTTCA                         GATGGGAAGAC-TTGTATANTGAATTGGAAGTTGTTGGAGGG-ATGAANCT
genomic: TCGCAAAGGCTATGGAGAAAGTTGGCAAAGAGGGAGTAATCACAATTTCAgtaagtcact ... attgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTG-AGGGGATGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattttttaaattgcactatatgtctaactctttccatggggaattgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA
                        gtctaac  putative branch site (score: 2)
     tttttaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactctttccatggggaattgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA

- - - - - - - - - - - - - - - - - - - - - tgctgaa