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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgctcagcaagctcgcttgttcatttgatatttgcgaactacatactttttgttcaatcttgtgttaagttgttattgtgatttcattattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAGCTTCAAAGGCGACTGCCTCCTGTTAATGCCTTTCGCCAAGGTCAAGGAG

Basic information

species Vitis vinifera
transcript Vv05s0020g04720.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 2
------tcatgctcagcaagctcgcttgttcatttgatatttgcgaactacatactttttgttcaatcttgtgttaagttgttattgtgatttcattattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAGCTTCAAAGGCGACTGCCTCCTGTTAATGCCTTTCGCCAAGGTCAAGGAG
      || | ||  | |   |      ||  ||  | |  |    |   |||  ||  |     ||| ||    || |  | |||||   |  ||| | |||||||| |||||  |||||||| ||||||||||||| || |||||||||||||| || ||||||||  ||||||   | | ||||    | |     ||   ||
aacctttcgtcctttgtagaatgcaaaattttttctagagattgagatggcat--ttgcttccacatcctg----aattcctgattgtatctaaattgtgggatagGTATTGCTGAGAGATCCAACAGATGAAAATGTGATCCCTGTTGTTGAGGAACTGCAAAGGCGGTTGCCTCAATTGAGTGCCACCGGTCTTCAACAGCAAG

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 2
---------tcatgctcagcaagctcgcttgttcatttgatatttgcgaactacatactttttgttcaatcttgtgttaagttgttattgtgatttcattattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAGCTTCAAAGGCGACTGCCTCCTGTTAATGCCTTTCGCCAAGGTCAAGGAG
         || |  | || | ||  | |||||   | || |||   ||  |    | ||  |     ||| ||    || |  | | |||   |  ||| | |||||||| |||||  |||||||| ||||||||||||| || |||||||||| ||| || ||||||||  ||||||   |   |||   ||   ||    ||||||
aacctttggtcctttttagaatgcatgattgttt-ctagagatt---gagatg-gcatttgcttccacatcctg----aactcctgaatgtatctaaattgtgggatagGTATTGCTGAGAGATCCAACAGATGAAAATGTGATCCCTGTTGTTGCGGAACTGCAAAGGCGGTTGCCTCGATTAGGTGCTGGTCTTAAACAGGAAGGAG

upper sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 3
tcatgctcagcaagctcgcttgttcatttgatatttgcgaactacatactttttgttcaatcttgtgttaagttgttattg---tgatttcattattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAGCTTCAAAGGCGACTGCCTCCTGTTAATGCCTTTCGCCAAGGTCAAGGAG
| ||      || |||   |  |  ||||   | |   | | | | ||        |   | ||| |||   || || | |   ||| ||     |   | |||| |||||||| ||||| || ||||||||||||||||| ||||| |||||||||| ||| ||  | |||  ||  ||||| |  | | | |||     ||
taatatcagccaggctt--tgatctatttagcact-atggaatgcttagaggagtatagcttttgagttctcttcttgtagtaatgacttgggcttattacagGTTTTGCTTCGGGATCCGTCTGATGAAAATGTTATTCCAGTTGTGGAGGAGCTTCGAAGACGCTTACCTGTTGGAAATGCATCACACAATGGTGGTCAAG

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|71857958|gb|DT007013.1|DT007013
EST:     CATATCAAGGCTATCATCACTGCTGAAGAG                         GTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
genomic: CATATCAAGGCTATCATCACTGCTGAAGAGgtcagttgtt ... tattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
EST: gi|161719350|gb|FC068970.1|FC068970
EST:     CATATCAAGGCTATCATCACTGCTGAAGAG                         GTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
genomic: CATATCAAGGCTATCATCACTGCTGAAGAGgtcagttgtt ... tattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
EST: gi|161717315|gb|FC065266.1|FC065266
EST:     CATATCAAGGCTATCATCACTGCTGAAGAG                         GTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
genomic: CATATCAAGGCTATCATCACTGCTGAAGAGgtcagttgtt ... tattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
EST: gi|71855947|gb|DT005002.1|DT005002
EST:     CATATCAAGGCTATCATCACTGCTGAAGAG                         GTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTT
genomic: CATATCAAGGCTATCATCACTGCTGAAGAGgtcagttgtt ... tattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTT
EST: gi|161717936|gb|FC069249.1|FC069249
EST:     CATATCAAGGCTATCATCACTGCTGAAGAG                         GTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
genomic: CATATCAAGGCTATCATCACTGCTGAAGAGgtcagttgtt ... tattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
EST: gi|71857515|gb|DT006570.1|DT006570
EST:     CATATCAAGGCTATCATCACTGCTGAAGAG                         GTGTTGCTCCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG
genomic: CATATCAAGGCTATCATCACTGCTGAAGAGgtcagttgtt ... tattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactttttgttcaatcttgtgttaagttgttattgtgatttcattattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAGCTTCAAAGGCGACTGCCTCCTGTTAATGCCTTTCGCCAAGGTCAAGGAG
                                       tttcatt  CT-rich tract
                                      atttcattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgctcagcaagctcgcttgttcatttgatatttgcgaactacatactttttgttcaatcttgtgttaagttgttattgtgatttcattattggatagGTGTTGCTTCGAGATCCATCAGATGAAAATGTTATTCCTGTTGTTGAGGAGCTTCAAAGGCGACTGCCTCCTGTTAATGCCTTTCGCCAAGGTCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
-catgctc
- - - - -gcaagct