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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaccttaccgtcagtttgtttacttagtttgaatggttgaggggtcctaattcattaagaggcgaaatctgtttaaataactcatcatttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGAAACTCAGATTTCAA

Basic information

species Vitis vinifera
transcript Vv07s0095g00730.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0095g00730.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G48680.1 (Arabidopsis thaliana), 3'ss of exon 1
-------tgcaccttaccgtcagttt-gtttacttagtttgaatggttgaggggtcctaattcattaagaggcgaaatctgtttaaataactcatcatttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTT---ATGAGGATGGTGAAACTCAGATTTCAA
          ||  | || |   |||    |   || | ||| || ||  | | |     || |   | | |||  ||  || | | || || ||  | |     |||    |||||||||||||| |||||||||||||||||||   | || ||||  ||  ||| | ||||||
acaatttcaaacagttccatagattttagctctgtattatgattgattttgtgat----gtttaaacaaaagcgtgatgagtattattacctaattgtatt----cagAGGAAGGCAAGATGATGATAAGTGGGAGCATGATCTTTTCGAAGACGATGACGAGCCTCGGCTTTCAA
















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|110387586|gb|EC952267.1|EC952267
EST:     GGAACCTCCTTAGACGATTCTGGCCGCAGGCGTCAGTTCACTGGCAAGAG                         GCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
genomic: GGAACCTCCTTAGACGATTCTGGCCGCAGGCGTCAGTTCACTGGCAAGAGgttcgttttc ... ttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
EST: gi|110392715|gb|EC957006.1|EC957006
EST:     GACGATTCTGGCCGCAGGCGTCAGTTCACTGGCAAGAG                         GCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
genomic: GACGATTCTGGCCGCAGGCGTCAGTTCACTGGCAAGAGgttcgttttc ... ttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
EST: gi|110403049|gb|EC964134.1|EC964134
EST:     ACTGGCAAGAG                         GCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
genomic: ACTGGCAAGAGgttcgttttc ... ttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
EST: gi|110700706|gb|EE077594.1|EE077594
EST:     ATTCTGGCCGCAGGCGTCAGTTCACTGGCAAGAG                         GCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA
genomic: ATTCTGGCCGCAGGCGTCAGTTCACTGGCAAGAGgttcgttttc ... ttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctaattcattaagaggcgaaatctgtttaaataactcatcatttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGAAACTCAGATTTCAA
                               aaataac  putative branch site (score: 2)
                                     ctcatcatttctct  CT-rich tract
                     aaatctgtttaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaccttaccgtcagtttgtttacttagtttgaatggttgaggggtcctaattcattaagaggcgaaatctgtttaaataactcatcatttctctgcagGCAGAGGCAAGATGATGACAAGTGGGAGCATGATCTTTATGAGGATGGTGAAACTCAGATTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
tgcacct
- - - - - - - - - - - - - - - -tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggcgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcatc