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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggtatatgtagttatgcttgctcttcaatgatagtactcttagtaataagtattcaaatgtatttttctacattttctttaaattcgtttttttccctatttttttttttttaatctaatattagttgcacttgatatgctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGTGGACTTGTTGCTGCTTCTGTGGTTGCTGACCCCTTTGAGTACTGTGATA

Basic information

species Vitis vinifera
transcript Vv04s0008g00770.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G09640.1 (Glycine max), 3'ss of exon 2
gtatgggtatatgtagttatgcttgctcttcaatgatagtactcttagtaataagtattcaaatgtatttttctacattttctttaaattcgtttttttccctatttttttttttttaatctaatattagttgcacttgatatgctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGTGGACTTGTTGCTGCTTCTGTGGTTGCTGACCCCTTTGAGTACTGTGATA
                                    ||    |  || | ||   | |||     |  |    | |  ||  | |||  |   | |      |||  |||| || ||     ||  ||| || ||  | ||| ||   |||||||||||||||  || ||||||||||| ||||||||||||||||| || ||||| ||||||||||| |||||  ||||| | ||||||||||| |||||||
-----------------------------------gtatgttttgtacttatgcattttctggaattataaattgctcttgatctaatatgtctctgcattatatggttttattcttggcaaaaagttaattacatcttatacgcatggaaagATTGCAGATGAAGTAGGTGCTTTTCTTATGATGGATATGGCTCATATAAGTGGGCTTGTTGCTGCATCTGTACTTGCTAATCCCTTTGAGTATTGTGATA

upper sequence: Vv04s0008g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G29410.1 (Glycine max), 3'ss of exon 6
gtatgggtatatgtagttatgcttgctcttcaatgatagtactcttagtaataagtattcaaatgtatttttctacattttctttaaattcgtttttttccctatttttttttttttaatctaatattagttgcacttgatatgctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGTGGACTTGTTGCTGCTTCTGTGGTTGCTGACCCCTTTGAGTACTGTGATA
                                    ||    |  || |  |   | |||     |  |    |||   |  | |||  |   | |      |||  |||| || ||     ||   || || |   | ||||||   | |||||||||||||  || ||||||||||| ||||||||||||||||| || ||||| ||||||||||| |||||  || || | ||||||||||| |||||||
-----------------------------------gtatgttttgtacttgtgcattttctggaattataaattactcatgatctaatatgtctctacattatatggttttcttcttggcaaaaagctaattacttcttatatgcatgggaagATTGCAGATGAAGTAGGTGCTTTTCTTATGATGGATATGGCTCATATAAGTGGGCTTGTTGCTGCATCTGTACTTTCTAATCCCTTTGAGTATTGTGATA

upper sequence: Vv04s0008g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S176_89V6.3 (Physcomitrella patens), 3'ss of exon 5
-------------------------gtatgggtatatgtagttatgcttgctcttcaatgatagtactcttagtaataagt---attcaa--atgtatttttctacattttctttaaattcgtttttttccctatttttttttttttaatctaatattagttgcacttgatat---gctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGTGGACTTGTTGCTGCTTCTGTGGTTGCTGACCCCTTTGAGTACTGTGATA
                          | |||   | ||  || | | | |  |    | |  |||  |   ||  ||  ||   |||     | | ||   | |  | |  |  | |||     |    |  |          |  |||       ||  | |     |   |   | |     ||||||| ||  | || || |||||||| |||||||| ||||| ||||||||||| |||||||| ||   |||  |     |||| ||||||||||| ||  
gtagaattcgtaccgtgggtccgcaatttggaggtttggtgtgagg-tggagcggggagggcagttgtgcgagggatgtgtcacattgtgtgaggcatgagtttgtagtggcagtgaatggcggtgaaacgatgcaacagacgtactaaaagtgggttgatggtttccggggtttgggtgatgtagATTGCGGACAGCGTGGGAGCTTTTCTGATGATGGACATGGCCCACATTAGTGGGCTTGTTGCAGCCGGTGTTCTAAGCAACCCGTTTGAGTACTGCGACG

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|71877324|gb|DT026379.1|DT026379
EST:     GCTTATCCTCGAGATTTTGATTATCCTCGTATGAGGAAG                         ATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
genomic: GCTTATCCTCGAGATTTTGATTATCCTCGTATGAGGAAGgtatgggtat ... gctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
EST: gi|110724687|gb|EE100735.1|EE100735
EST:     CTGGTGCTAGTGCTTATCCTCGAGATTTTGATTATCCTCGTATGAGGAAG                         ATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
genomic: CTGGTGCTAGTGCTTATCCTCGAGATTTTGATTATCCTCGTATGAGGAAGgtatgggtat ... gctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
EST: gi|110390273|gb|EC955175.1|EC955175
EST:     TTTTGATTATCCTCGTATGAGGAAG                         ATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
genomic: TTTTGATTATCCTCGTATGAGGAAGgtatgggtat ... gctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
EST: gi|110384184|gb|EC948603.1|EC948603
EST:     TTTTGATTATCCTCGTATGAGGAAG                         ATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
genomic: TTTTGATTATCCTCGTATGAGGAAGgtatgggtat ... gctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
EST: gi|110385950|gb|EC950512.1|EC950512
EST:     TTTTGATTATCCTCGTATGAGGAAG                         ATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT
genomic: TTTTGATTATCCTCGTATGAGGAAGgtatgggtat ... gctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctatttttttttttttaatctaatattagttgcacttgatatgctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGTGGACTTGTTGCTGCTTCTGTGGTTGCTGACCCCTTTGAGTACTGTGATA
     atttttttttttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgggtatatgtagttatgcttgctcttcaatgatagtactcttagtaataagtattcaaatgtatttttctacattttctttaaattcgtttttttccctatttttttttttttaatctaatattagttgcacttgatatgctctgaaagATTGCAGATGGTGTTGGTGCTTTTCTCATGATGGATATGGCTCACATTAGTGGACTTGTTGCTGCTTCTGTGGTTGCTGACCCCTTTGAGTACTGTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT