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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttcatgctgaatttattgtccacaggagtcgatcaggaataattaaccaatttcttgtctggatagatttcactttgatcagggcttagcatag...

Basic information

species Vitis vinifera
transcript Vv08s0007g06480.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G29260.1 (Glycine max), 5'ss of exon 6
ATGGGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttcatgctgaatttattgtccacaggagtcgatcaggaataa--ttaaccaatttcttgtctggatagatttcactttgatcagggctta-gcatag--
 |||| | || || ||| |  |||||||||||||||| ||||| ||||||||||||||||| |         |||  | | | ||| || ||     ||||  || |   || | |   || | |||||  |  |     ||| ||| | |   |   
GTGGGAGCTTTCAAAGACTCTTCATGATTTCTTATCTCGATGAGGAGATACTTgtaagtttaacata----ctatcattctccggaatcaattttagataaatttgatgcatgtgtacccttg-tagatgactatgctgacagagctaatgtgaaatc

upper sequence: Vv08s0007g06480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA09G17130.1 (Glycine max), 5'ss of exon 6
ATGGGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttcatgctgaatttattgtccacaggagtcgatcaggaataattaaccaatttcttgtctggatagatttcactttgatcagggctta-gcatag--
 |||  | || |||||| |  |||||||||||||||| ||||| ||||||||||||||||| |   |    | ||| ||   |  |     | ||  | || | |   || | |   || | | |||  || ||    ||| ||| | |   |   
GTGGAAGCTTTCAGAGACTCTTCATGATTTCTTATCTCGATGAGGAGATACTTgtaagtttaaca-tactctcattttctggaataagtt-ttagataaaactgatgcatgtatgcccttg-tggatgacaattctcacagagctaatgtgaaatc

upper sequence: Vv08s0007g06480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G42130.2 (Arabidopsis thaliana), 5'ss of exon 6
ATGGGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttcatgctgaatttattgtccacaggagtcgatcaggaataattaaccaatttcttgtctggatagatttcacttt-gatcagggcttagcatag----
 |||    ||  | ||| |  ||||||| |||||||| ||||||||||| |||||||||||   | ||||| | ||||  | |   || ||    || | |   | |  |    |  | |  |    | | |||| | |      ||  | |||    
GTGGATCCTTTGAAAGATTTTTCATGATATCTTATCTAGATGAAGAGATTCTTgtaagttt---gttgaatattttgttaagaatggt-gagagagactga--gatcgttgcactaaccgagttttatccgcttttggttgttttttctcgtagatag

upper sequence: Vv08s0007g06480.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G42130.3 (Arabidopsis thaliana), 5'ss of exon 6
ATGGGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttcatgctgaatttattgtccacaggagtcgatcaggaataattaaccaatttcttgtctggatagatttcacttt-gatcagggcttagcatag
 |||    ||  | ||| |  ||||||| |||||||| ||||||||||| |||||||||||   | ||||| | ||||  | |   || ||    || | |   | |  |    |  | |  |    | | |||| | |      ||  | |||
GTGGATCCTTTGAAAGATTTTTCATGATATCTTATCTAGATGAAGAGATTCTTgtaagttt---gttgaatattttgttaagaatggt-gagagagactga--gatcgttgcactaaccgagttttatccgcttttggttgttttttctcgtag

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|110417321|gb|EC983367.1|EC983367
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCGAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|110374942|gb|EC939888.1|EC939888
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|110423470|gb|EC989816.1|EC989816
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCGAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|110359681|gb|EC921566.1|EC921566
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|110388670|gb|EC953446.1|EC953446
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|110375169|gb|EC940130.1|EC940130
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|110384614|gb|EC949066.1|EC949066
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
EST: gi|18458755|gb|BM437033.1|BM437033
EST:     GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTT                         ATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG
genomic: GGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttca ... tttaatgcagATACTGAGGGATACTACCGGAATACCCGAAGTTCTTTCAAGGTTGGATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGCGTTTCCAGAGAATGCTCATGATTTCTTATCTTGATGAAGAGATACTTgtaagtttcatgctgaatttattgtccacaggagtcgatcaggaataattaaccaatttcttgtctggatagatttcactttgatcagggcttagcatag

- - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaata