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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttacaattttctgttctttccttttctaggataaacagcttctgcatttgggctctgaacttagaatatgtttgatttcgttttatgctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGATTAGTGGCAGAGAAAGAAGGTGTTCTTGATGGGTTTCGTGTAGTCATCA

Basic information

species Vitis vinifera
transcript Vv01s0011g01610.t01
intron # 4
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|34362915|gb|CF404500.1|CF404500
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|110389333|gb|EC954162.1|EC954162
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|349818483|gb|FQ403118.1|FQ403118
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|110384323|gb|EC948751.1|EC948751
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|71867299|gb|DT016354.1|DT016354
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|71867022|gb|DT016077.1|DT016077
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|349818522|gb|FQ403157.1|FQ403157
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
EST: gi|110379724|gb|EC944942.1|EC944942
EST:     ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAG                         GCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA
genomic: ATGTTTTAGTCATTCCAAAGTTAAGAGATGGATTGACACAGCTTGGAAAGgttatattta ... gctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatttgggctctgaacttagaatatgtttgatttcgttttatgctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGATTAGTGGCAGAGAAAGAAGGTGTTCTTGATGGGTTTCGTGTAGTCATCA
                            gtttgat  putative branch site (score: 5)
                                              ctttgtc  putative PPT
                       aatatgtttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttacaattttctgttctttccttttctaggataaacagcttctgcatttgggctctgaacttagaatatgtttgatttcgttttatgctttgtcagGCTGAAGTAAGACATGAACAGATACTGGGTCAACTTCTCTATGCAGCCAGATTAGTGGCAGAGAAAGAAGGTGTTCTTGATGGGTTTCGTGTAGTCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - tctttcc
- - - - - - - - - - - - - - - - ggataaa
- - - - - - - - - - - - - - - - - - - -cagcttc
- - - - - - - - - - - - - - - - - - - - - - - -gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgaa