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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttttttgtcgatttttgagctagcgttgttgataatttatttccctgaaacattgttctattttgtaggtaaatgttgtattcttgttttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCTAGATTTGTATTGTGGAATGGTAAATTGAGGCCGGTTCCCTCCAAGCCAA

Basic information

species Vitis vinifera
transcript Vv07s0005g02540.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 1
ctgttttttgtcgatttttgagctagcgttgttgataatttatttccctgaaacattgtt-ctattttgtaggtaaatgttgtattcttgttt---tcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCTAGATTTGTATTGTGGAATGGTAAATTGAGGCCGGTTCCCTCCAAGCCAA
   |||||      |  | |||       |    ||| | | | ||    |  | | |    |   |||| ||||| ||| || ||  | |||   | | ||||||||| |||||||| |||||||| |||||||||||||||||| |||||||| | ||||| ||||||||  | || ||||||||||| |||   ||||  |
---tttttaactattagtagagtgtctagtaaaaatagtgtgtctctagcactcctcgcagttgaattgttggtaa-tgtagttttggtttttgcatttggcagGTGGACAGTGGTTTAAAGGATGAGCTTGTTTTGGGGGATCCTGATGCACCTCGGTTTGTGTTGTGGAACAGGAAGTTGAGGCCGGTGCCCGGGAAGCTGA

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 2
ctgttttttgtcgatttttgagctagcgttgttgataatttatttccctgaaacattgttctatt---ttgtaggtaaatgttgtattcttgttt---tcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCTAGATTTGTATTGTGGAATGGTAAATTGAGGCCGGTTCCCTCCAAGCCAA
    ||||      |  | ||||  |   |    |||  || | |  ||   ||   |     ||   |||| ||||| ||| || |   | |||   | | ||||||||| ||||| || |||||| | |||||||||||||||||| |||||||| | ||||| ||||||||||| || |||||||| || ||    ||||| |
---attttaactattagtagagcgggtactacaaata--ttgtgtagctagcactccgcatagttgaattgttggtaa-tgtggtttcggtttttgcatttggcagGTGGACAGTGGCTTAAAGGATCAGCTTGTTTTGGGGGATCCTGATGCACCTCGGTTTGTGTTGTGGAATGGGAAGTTGAGGCCAGTGCCTGGGAAGCCGA

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 1
-ctgttttttgtcgatttttgagctagcgttgttgataatttatttccctgaaacattgttctattttgtaggtaaatgttgtattcttgtt-ttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCTAGATTTGTATTGTGGAATGGTAAATTGAGGCCGGTTCCCTCCAAGCCAA
     || |||      | |||        |  ||| ||   || |   ||  | ||||||  ||||      | |   || | |  || |  ||   | |||| ||||||||||||||||||||| | || ||||| ||||||| ||| || || ||||| ||||||||||| ||||||||||||||||| || |||| ||
gtaagttcttgaaacaatctgattcgttaatactgagaaca-atgtatttgtga-attgtttgatttgtggatttagccttctctgtttatggttagagtagGTAGATAGTGGTTTGAAGGATGATTTGGTGTTGGGAGATCCTACTGCGCCAAGGTTTGTGTTGTGGAATGGGAAATTGAGGCCGGTTCCATCGAAGCTAA

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|352782141|gb|FQ470043.1|FQ470043
EST:     AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCC                         GTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
genomic: AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCCgtaagttttg ... tttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
EST: gi|352782117|gb|FQ470019.1|FQ470019
EST:     AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCC                         GTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
genomic: AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCCgtaagttttg ... tttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
EST: gi|352764041|gb|FQ467611.1|FQ467611
EST:     AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCC                         GTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
genomic: AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCCgtaagttttg ... tttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
EST: gi|352764189|gb|FQ471169.1|FQ471169
EST:     AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCC                         GTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT
genomic: AGGAAGGCCCCAACAGCTTCCAGCCCTCCGATTCCATGCTCACCATGGCCgtaagttttg ... tttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgaaacattgttctattttgtaggtaaatgttgtattcttgttttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCTAGATTTGTATTGTGGAATGGTAAATTGAGGCCGGTTCCCTCCAAGCCAA
                                    tattcttgttttctt  CT-rich tract
             ttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttttttgtcgatttttgagctagcgttgttgataatttatttccctgaaacattgttctattttgtaggtaaatgttgtattcttgttttcttgcagGTGGATAGTGGTTTGAAGGATGATCTTGTTTTGGGGGATCCTAATGCACCTAGATTTGTATTGTGGAATGGTAAATTGAGGCCGGTTCCCTCCAAGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - -gaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggtaaa