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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacatgttaagaaccctgacttattgactgaagaaaatttctagttctttctgcagatgtgtttgtatgatgtttttttccttgcatattctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCCTTCTATGCATTCATCTCTTTTTGGAGCAATTGAATTGTCTAAAAAGCATGGTGGGCTTG

Basic information

species Vitis vinifera
transcript Vv08s0007g01640.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01640.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G14960.1 (Glycine max), 3'ss of exon 4
--------atacatgttaagaaccctgacttattgactgaagaaaatttctagttctttctgcaga-tgtgtttgtatgatgtttttttccttgcatattctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCCTTCTATGCATTCATCTCTTTTTGGAGCAATTGAATTGTCTAAAAAGCATGGTGGGCTTG
        ||  | |   |  || ||   | || |||     |   || |  ||  |   || | | ||  |||||    |||  ||    |||  |   ||  ||||||| ||||||||||| || |||||||| ||||||||||  || || ||| | ||| | || ||  |||||||| | | | |||| |||  ||  || ||||
ttttgttaatgtaggaggaagactcttcttcatcgac-----atgtttgcccgtgttaagtgtaaactgaatttgt----tgtgattgcttttgtgtggactactgcagGCAAGGATTTTCCATTTCAATTCAGAAGTTCTAACATGCCCCTCGATGGAATCAACCCTATTCAGAGCAATTAAGTGGACTAAGAAGTTTGACGGCCTTG
















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|349808719|gb|FQ406446.1|FQ406446
EST:     CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAG                         GCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCCTTCTATGCAT
genomic: CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAGgtaatctgaa ... tctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCCTTCTATGCAT
EST: gi|349824091|gb|FQ417478.1|FQ417478
EST:     CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAG                         GCCAGGATTTTCCACTTTAATTCAAAAGGT-CTAACATCGCCT
genomic: CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAGgtaatctgaa ... tctcttgcagGCCAGGATTTTCCACTTTAATTCAGA-GGTTCTAACATCGCCT
EST: gi|351027686|gb|FQ446853.1|FQ446853
EST:     CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCNAAGAG                         GCCAGGATTTTCCACTTTAATTCAGAGGTTCTAAC
genomic: CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAGgtaatctgaa ... tctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAAC
EST: gi|351029547|gb|FQ427387.1|FQ427387
EST:     CAGAGGATTCTCTCCTCAACTCTGAACTCAACATTGCCGTGCTCAAAGAG                         GCCAGGATTTTCCACTTTAATTTC-GAAGGTTCTACC-TCGCCTTCTATGC
genomic: CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAGgtaatctgaa ... tctcttgcagGCCAGGATTTTCCACTTTAATT-CAGA-GGTTCTAACATCGCCTTCTATGC
EST: gi|351019740|gb|FQ439557.1|FQ439557
EST:     CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAG                         GCCAGGATTTTCCACTTTAATT
genomic: CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAGgtaatctgaa ... tctcttgcagGCCAGGATTTTCCACTTTAATT
EST: gi|349827207|gb|FQ421480.1|FQ421480
EST:     CAGAGGATTCTCTCCTCAGCTCTGATCTCAACATTGCCGTGCTCAAAGAG                         GCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCC
genomic: CAGAGGATTCTCTCCTCAGCTCTGAACTCAACATTGCCGTGCTCAAAGAGgtaatctgaa ... tctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttctgcagatgtgtttgtatgatgtttttttccttgcatattctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCCTTCTATGCATTCATCTCTTTTTGGAGCAATTGAATTGTCTAAAAAGCATGGTGGGCTTG
                            tttttttccttgcata  CT-rich tract
                     tatgatgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacatgttaagaaccctgacttattgactgaagaaaatttctagttctttctgcagatgtgtttgtatgatgtttttttccttgcatattctcttgcagGCCAGGATTTTCCACTTTAATTCAGAGGTTCTAACATCGCCTTCTATGCATTCATCTCTTTTTGGAGCAATTGAATTGTCTAAAAAGCATGGTGGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- acatgtt
- - - - - - - ccctgac
- - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - tctgcag