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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaagctctagttatcgtgaatttttaagtgcgcgtgagcatgcacatgggagtctctgtgcattttttgtaactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC

Basic information

species Vitis vinifera
transcript Vv17s0000g00160.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 1
taaagctctagtta-tcgtgaatttt-taagtgcgcg---tgagcatgcacatgggagtctctgtgcattttttgtaactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC
||    |  | ||  | ||| ||||  ||| |        |||   | |  |||   |   ||  | |||||    | |  || |  |||||| |    |||||||| || ||| |||||||||| |||||||| ||||| ||||| |||||||| || ||  |||| |||||||||||||| ||||| || ||||| ||||| |
tatgtttgaaattgcttgtgtatttgataactttttattttgattttacttatgttgggtactaag-attttagtcaccaaattcattcttttct----tttcagCACTTCGTTTTGGAGGAGAACATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTGTTGAAGGCATCGGGGCATGTCGAGAAGTTTACTGACC

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 1
taaagctctagttatcgtgaatttttaagtgcgcgtgagcatgcacatgggagtctctgtgcattttttgt---aactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC
    | | |  ||  | |   ||| | | | |  |||       |      |   |||     || ||||       |  |    |  || || |     ||||| |||||| |||| |||||||||||||| ||||| ||||| |||||||| || ||  |||| |||||||||||||| ||||| || ||||| ||||| |
--gtgttgtgatttgc-tagttttgttatttcttgtggttgatgattcatcatgttctactttttctttgctaaggttactgatattcttaatttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G821551_T03 (Zea mays), 3'ss of exon 1
taaagctcta-gttatcgtgaatttttaagtgcgcgtgagcatgcacatgggagtctctgtgcattttt-tgtaactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC
 ||    |||  || | || | || ||  ||    | ||     ||  | | | | |   |    |    |   | |  |    | ||| || |   | ||||| |||||| |||| ||||| |||||||| ||||| ||||| |||||||| || ||  |||| ||||||||||| || |||||||| ||||| ||||| |
gaactgactacattttagttatttctt--gtagttgagattcatcatgttgtacttttcctttgctaagataagattactgatatatttaatttctctccagCACTTTGTTTTGGAAGAGAACATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCAGGCCATGTTGAGAAGTTTACTGACC

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|352781854|gb|FQ469152.1|FQ469152
EST:     GCCCTCCCGGTTGCGCCGTCAAGTCCAATGTTCTCGCCTTCTGGCGTCAG                         CATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACA
genomic: GCCCTCCCGGTTGCGCCGTCAAGTCCAATGTTCTCGCCTTCTGGCGTCAGgttaattttt ... attgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACA
EST: gi|71855426|gb|DT004481.1|DT004481
EST:     GCCCTCCCGGTTGCGCCGTCGAGTCCAATGTTCTCGCCTTCTGGCGTCAG                         CATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACA
genomic: GCCCTCCCGGTTGCGCCGTCAAGTCCAATGTTCTCGCCTTCTGGCGTCAGgttaattttt ... attgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgggagtctctgtgcattttttgtaactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC
                                tcccctcttttatatt  CT-rich tract
                                     tcttttatattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaagctctagttatcgtgaatttttaagtgcgcgtgagcatgcacatgggagtctctgtgcattttttgtaactgatcccctcttttatattgtttcagCATTTTGTTCTGGAGGAGAATATGTTGGAAGTTGATTGCCCATGTGTGACACCAGAAATTGTATTGAAGGCATCGGGTCATGTTGATAAGTTCACTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - gcgcgtg
- - - - - - - - - - - - - - - - - - - -catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt