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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcctgctcctttcccctttttcttttttgagattttgtgattatctaggtgaaagtatttatattcttatttacttcaaaatttctttcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTGATAGTTAACTTGCCAATAGATGTATTGCAAGTTATGAGACATAATTTTC

Basic information

species Vitis vinifera
transcript Vv04s0023g01400.t01
intron # 1
splice site 3'
intron type U2

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|351013468|gb|FQ425499.1|FQ425499
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|351017481|gb|FQ435834.1|FQ435834
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|349829422|gb|FQ419954.1|FQ419954
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTAGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|351020019|gb|FQ439836.1|FQ439836
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|351022951|gb|FQ428860.1|FQ428860
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|351017004|gb|FQ424431.1|FQ424431
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|161716246|gb|FC066848.1|FC066848
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATG                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
EST: gi|351040005|gb|FQ425091.1|FQ425091
EST:     TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATA                         GTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG
genomic: TCCGAAGCCGACAAGCTTCCTTCCACAGATACGTGCATTTGGAGCTTATAgtaagtcact ... tcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctaggtgaaagtatttatattcttatttacttcaaaatttctttcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTGATAGTTAACTTGCCAATAGATGTATTGCAAGTTATGAGACATAATTTTC
                                       tttctttcttgatc  CT-rich tract
         aaagtatttatattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattcctgctcctttcccctttttcttttttgagattttgtgattatctaggtgaaagtatttatattcttatttacttcaaaatttctttcttgatcagGTTTCAGAGTTTTCTGTACTTCAGTGTTGAGAGGTGAATAGGGAATCGTTGATAGTTAACTTGCCAATAGATGTATTGCAAGTTATGAGACATAATTTTC

- - cctgctc
- - - - - -ctttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagta