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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtctatttccattcctatcccctttcaccagcctcacctttagttcttttgacttaaattttaactgctaatatcagtttaatttctgttatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCTACTTCCAGAATTATTAGACCTATTGGGAGCCTTTCACTTTGTTGAACCT

Basic information

species Vitis vinifera
transcript Vv18s0122g00430.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 3
-------agtctatttccattcctatcccctttcaccagcctcacctttagttcttttgacttaaattttaactgctaatatcagtttaatttctgttatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCTACTTCCAGAATTATTAGACCTATTGGGAGCCTTTCACTTTGTTGAACCT
       |   ||||        |       || |        | |||||    | |||  | ||  |||   |  | |||  | |||||  ||| ||||   | || ||||||||| ||||||| || ||||||||||||||| || | ||||||||  |||| ||| ||||||||||||||||||||||||||||||| ||||| 
ttgatagaacatattatataaaatgaaaatgtttattgatgatatcttta----tattgtgtgaagctttgtata-tgata--attttaacctcttttatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCTGATTCCTGAAATATTAGACCTATTGGGAGCCTTTCACTTTGTAGAACCA

upper sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G39750.1 (Glycine max), 3'ss of exon 1
-------agtctatttccattcctatcccctttcaccagcctcacctttagttcttttgacttaaattttaactgctaatatcagtttaatttctgttatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCTACTTCCAGAATTATTAGACCTATTGGGAGCCTTTCACTTTGTTGAACCT
       |   ||||        |       || |  |     |  ||||  |||| ||   | ||| ||      ||  |||| || ||  ||| ||||   | || ||||||||| ||||||| || |||| || |||||||    |  ||||| |  ||||  || ||||| |||||||||||||| |||||||||| ||||||
ttgacagaacatattatataaaatgaatatgtttattaatactatattta--tcttgtg---tgaatctttgta--tatgatcatttaaacctcttttatccataagCTTTGAGATATTGCATGCTCGGTGGGTTACGCTTGCATTTGTCAGTGCTGTGATTCCTAAAATATTAAACCTATTGGGAGCCGTTCACTTTGTAGAACCT
















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|349823595|gb|FQ415005.1|FQ415005
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
EST: gi|161718087|gb|FC067604.1|FC067604
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
EST: gi|122690646|gb|EC955583.1|EC955583
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
EST: gi|161714259|gb|FC063523.1|FC063523
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
EST: gi|349814847|gb|FQ410070.1|FQ410070
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
EST: gi|122690609|gb|EC954944.1|EC954944
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
EST: gi|110421925|gb|EC988231.1|EC988231
EST:     GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAA                         TTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT
genomic: GATATTGCTGGTCTGGGCAAGGATCCTGTGGCTTTCCAAAAATATTTCAAgtatgtcatg ... tatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgacttaaattttaactgctaatatcagtttaatttctgttatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCTACTTCCAGAATTATTAGACCTATTGGGAGCCTTTCACTTTGTTGAACCT
                                      tttctgttatttttc  CT-rich tract
                        taatatcagtttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtctatttccattcctatcccctttcaccagcctcacctttagttcttttgacttaaattttaactgctaatatcagtttaatttctgttatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCTACTTCCAGAATTATTAGACCTATTGGGAGCCTTTCACTTTGTTGAACCT

- - - - tccattc
- - - - - - - -ctatccc
- - - - - - - - - - - - ttcacca
- - - - - - - - - - - - - - - - cctcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctaa