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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC

Basic information

species Vitis vinifera
transcript Vv16s0098g01540.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g35810.1 (Oryza sativa), 3'ss of exon 1
ttttcttcagtcatccatgttctttctaactaatttatttctgtt-actgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC
  ||||  | |||| |  |        |  || |||  || | || | ||    |     |    |     | ||  ||   ||||  ||   |||   ||||| |||||||| |||||||||| || ||| | || ||||| || ||||| || ||||| || ||||| |||||||| || |||||||||||| |||| |
-cttctaaactcattctagcctcccagagttatttttcttttcttcaatggctttatgtcttcctaaaataacatcataccctgtttgctctggttgttagAGGTTGCCTCCACTGTCCACAGAGCCAAACAGATGCGAGCGTGCTTTTGTCGGGAACACAATTGGTCAGGCAAATGGGGTGTATGACAAGCCACTCGATC

upper sequence: Vv16s0098g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G13640.1 (Glycine max), 3'ss of exon 2
-----ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC
        | |  | |  |  | |     | | | | |   || |||   |  |  || | ||| ||     |  |      |  ||||| || |     |||||||||| || |||||||| || || ||||| ||||||||||| ||||||||||| ||||| || ||||| |||||||| || ||||| || ||| | || |
agcaaaagtttaaatttgtgaaagacaaatgtgatttacacatgtcttcaaaagaagcagttgaggagagaatgcaacacccactatgttttcct-----tgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC

upper sequence: Vv16s0098g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G41210.1 (Glycine max), 3'ss of exon 2
-----ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC
        | |  | |  |  | |     | | | | |   || |||   |  |  || | ||| ||     |  | | |     || |||| ||    |||||||| || || |||||||| || || ||| | ||||||||||| |||||| |||| ||||| || ||||| |||||||| || ||||| || ||| | || |
aatgaaagtttaaatttgtgaaagacaaatgtgatttacacatctcttcaaaagaagcagttgaggagagaatgca-acacc-caat-ttgttttcc--ttgcagAGACTTCCCCCATTGTCAACTGAGCCCCATCGCTGTGAGCGTGCATTTATTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC

upper sequence: Vv16s0098g01540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G53490.3 (Arabidopsis thaliana), 3'ss of exon 2
ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatg----atgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC
 | | |    | ||    |  ||||||  ||  | ||| | |||  |||  | ||   |||    |  || |  | | ||    |  | |  |  | ||| ||||| || ||||| || || ||||||||  |||| |||||    ||||||||||| |||||||| |||||||||||||| || |||||||| ||| | || |
gtctgtcacattatatg-gccctttct--cttttctatgtttgtgtctgaagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC

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|110694090|gb|EE070894.1|EE070894
EST:     TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAG                         AGGCTGCCTCCATTGTCCACAGAGCCCAACCGCTGTGAGCGGGCATTTGTT
genomic: TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAGgttaagagca ... atgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTT
EST: gi|349828381|gb|FQ416334.1|FQ416334
EST:     TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAG                         AGGCTGCCTCCATTGTCCACAGAGCCCAATCGCTGTGAGCGGGCATTTGTT
genomic: TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAGgttaagagca ... atgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTT
EST: gi|351044239|gb|FQ447593.1|FQ447593
EST:     TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAG                         AGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTT
genomic: TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAGgttaagagca ... atgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTT
EST: gi|349821222|gb|FQ408809.1|FQ408809
EST:     TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAG                         AGGCTGCCTCCATTGTCCACAGAGCCCAATCGCTGTGAGCGGGCATTTGTT
genomic: TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAGgttaagagca ... atgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTT
EST: gi|18458877|gb|BM437155.1|BM437155
EST:     TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAG                         AGGCTGCCTCCATTGTCCACAGAGCCCAATCGCTGTGAGCGGGCATTTGTT
genomic: TTGCTGTTTGTGCCGTGACTGCTGCCTCGCCTGTCATTGCTGCCAGTCAGgttaagagca ... atgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC
        tgctgat  putative branch site (score: 3)
                        tatatattatgatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - tcatcca
- - - - - - - - - - - - - -aactaat
- - - - - - - - - - - - - - - - - - - - - - -actgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtc