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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagccatagcattgtgaatttcttgtttgaagtatcatttgtttaatgtggtacattaggtttactttggtacaatataatttttcctttcttgttttttttttttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGGGTGGGCAATTGACAGAATTCTTCAGAAACATCAAAGGCACTATCGATGA

Basic information

species Vitis vinifera
transcript Vv04s0008g04520.t01
intron # 35
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 35
lower sequence: LOC_Os01g40990.2 (Oryza sativa), 3'ss of exon 34
gtagccatagcattgtgaatttcttgtttgaagtatcatttgtttaatgtggtacattaggtttactttggtacaatataatttttcctttcttgtttttttt-ttttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGGGTGGGCAATTGACAGAATTCTTCAGAAACATCAAAGGCACTATCGATGA
|||   || | |   | ||| | ||| |   | | |  |    ||||| |   |   || | |||   ||| ||| |  ||| |   |  ||  ||  |||   ||| ||  ||||||||||||||||||||||||| || ||||| ||||| || |||||||| ||||| |||||||| || || || |  ||||| | ||| || || |||||
gtacttattgaa--atcaatat-ttgctcctaattttgtggaattaatattccaagatatgcttatcgtgg-aca-tggaatctacacactcaagtactttccatttctttacagCTGTTGATATATATGCTGGTGTGGCAGCATCCCTTGCAGAAAGAAAAAAAGGTGGCCAATTGACTGAGTTTTTGAAGAACATAAGAGGAACCATAGATGA

upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 35
lower sequence: GLYMA06G07850.2 (Glycine max), 3'ss of exon 34
gtagccatagcattgtgaatttcttgtttgaagtatcatttgtttaatgtggtacattaggtttactttggtacaatataatttttcctttcttgttttttttttttttg-gcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGGGTGGGCAATTGACAGAATTCTTCAGAAACATCAAAGGCACTATCGATGA
       || |||||  | |||| | |||  | | |  |||  ||    ||     |||| |  ||   |          ||  ||   |  || |||| | || | |   |||||||||||||||||||| |||||||||||||| ||||||||||||||||  ||  | ||||||||||||||||| ||||||||||| ||||| || |||||
------gtaacattg--attttcctctttacaatctggttttgttgtcttgtgtttttagctccacaaagtgttgtcggcatacttagctagtttttttgtattgtatcatgcagCTGTTGATATATATGCCGGTGTTGCTGCATCTCTTGCTGAGAGAAAAAGAGGCAGCCAATTGACAGAATTCTTTAGAAACATCAAGGGCACAATAGATGA

upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 35
lower sequence: GLYMA04G07760.1 (Glycine max), 3'ss of exon 5
gtagccatagcattgtgaatttcttgtttgaagtatcatttgtttaatgtggtacattaggtttactttggtacaatataatttttcctttcttgttttttttttttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGGGTGGGCAATTGACAGAATTCTTCAGAAACATCAAAGGCACTATCGATGA
                       |    |  | | || | | |  ||| ||||   |||| |  ||   |       |  ||  ||   |  || ||||  || | | | ||||||||||||||||||||  ||||||||||||| ||||||||||||||||  ||  | ||||||||||||||||| ||||||||||| ||||| || |||||
----------------------gtaacattgattttcctctttacaatctggtt--ttagctccacaaagtgttgtcagcatacttagctagtttttttaattgtatcttgcagCTGTTGATATATATGCCAGTGTTGCTGCATCTCTTGCTGAGAGAAAAAGAGGCAGCCAATTGACAGAATTCTTTAGAAACATCAAGGGCACAATAGATGA

upper sequence: Vv04s0008g04520.t01 (Vitis vinifera), 3'ss of exon 35
lower sequence: AT2G25730.2 (Arabidopsis thaliana), 3'ss of exon 32
gtagccatagcattgtgaatttcttgtttgaagta-tcatttgtttaatgtggtacattaggtttactttggtacaatataatttttcctttcttgttttttttttttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGGGTGGGCAATTGACAGAATTCTTCAGAAACATCAAAGGCACTATCGATGA
                                ||  | |||||||| ||||   | ||  |  | |  ||| |     ||  | | |   ||    ||   ||  || |  |||||||||||||||||||||||||||||| | ||||| ||||| || || || ||  | || ||||||||| | |||| |||||| || || || ||| | ||
--------------------------------gtgcttatttgttttatgtta-atatctgtgtaatgttgttgtg-catggtatctgactt----ttcccttgcttctaagcagCTGTTGATATATATGCTGGTGTTGCTACGTCACTAGCTGATAGGAAGAAAGGCAGTCAGTTGACAGAACTTTTCAAAAACATTAAGGGAACAATCCAGGA

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|349809889|gb|FQ398514.1|FQ398514
EST:     CCGACTGATATATGAATTCAATCTTCCTG                         CTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGG
genomic: CCGACTGATATATGAATTCAATCTTCCTGgtagccatag ... tttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGG
EST: gi|349807218|gb|FQ401210.1|FQ401210
EST:     CCGACTGATATATGAATTCAATCTTCCTG                         CTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGG
genomic: CCGACTGATATATGAATTCAATCTTCCTGgtagccatag ... tttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttactttggtacaatataatttttcctttcttgttttttttttttttggcagCTGTTGATATATATGCTGGTGTTGCTGCATCACTTGCTGAGAGAAAAAAGGGTGGGCAATTGACAGAATTCTTCAGAAACATCAAAGGCACTATCGATGA
                 tataatttttcctttc  CT-rich tract
            tacaatataatttttc  TA-rich tract