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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagagtttatgttatcagcatactccatagtccatgttttattttctaataattgaccttcaaagcatgtattaattgcctgttgtttacttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 8
-------cagagttt-atgttatcagcatactc--catagtc----catgttttattttctaataattgacctt----caaag-----catgtattaattgcctgttgtttacttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
        ||| |||  | ||| |    | |||  |  ||||    |||| ||   |||   |     |   ||    |||||     ||  |  | |||  ||||| ||   | |||||||||||||| || |||||||||||||| ||||| ||||| 
gtatgtgtagaattttgttttagcgaagttctcatctgagtcaaggcatgcttctctttaatagggaaggtattacaacaaagtagcccaaatcattatttactgtttttctttattttgcagAATTATTCGAGATATTATTCAAAACCATCTGCTGCAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 8
-cagagtttatgttatcagcatactccatagtccatgttttattttctaataattgaccttcaaagcatgtattaattgcctgtt-gtttacttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
  |    ||   || | ||  | || | |  ||    | |    |  |||| |     |  ||   ||| |  | ||  | | ||   ||  |      |||||| |||||||||||||||||||| ||||| || || 
gtaatactttctttttgagtgt-cttcttgttcttcatatagggtcttaatgagatgacaccagttcattt-ctgatgacatcttcacttcttgccacacagAATAATCCGTGATATTATTCAAAACCATCTGCTACAG
















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|30299156|gb|CB975950.1|CB975950
EST:     AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG                         AATTATCCGTGATATTATTCAAAATCATCTACTGCGA
genomic: AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccatt ... ttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
EST: gi|294967142|gb|GW840017.1|GW840017
EST:     AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG                         AATTATCCGTGATATTATTCAAAATCATCTACTGCAA
genomic: AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccatt ... ttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
EST: gi|110696408|gb|EE072500.1|EE072500
EST:     AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG                         AATTATCCGTGATATTATTCAAAATCATCTACTGCAA
genomic: AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccatt ... ttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
EST: gi|110364929|gb|EC928538.1|EC928538
EST:     AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG                         AATTATCCGTGATATTATTCAAAATCATCTACTGCAA
genomic: AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccatt ... ttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
EST: gi|56409520|gb|CX017772.1|CX017772
EST:     AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG                         AATTATCCGTGATATTATTCAAAATCATCTACTGCAA
genomic: AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccatt ... ttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
EST: gi|110372969|gb|EC937167.1|EC937167
EST:     AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG                         AATTATCCGTGATATTATTCAAA-TCATCTACTGCAAGT
genomic: AGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGGgtatgccatt ... ttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaataattgaccttcaaagcatgtattaattgcctgttgtttacttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA
                        tattaat  putative branch site (score: 2)
                                     ttgtttactttttt  putative PPT
                                     ttgtttactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagagtttatgttatcagcatactccatagtccatgttttattttctaataattgaccttcaaagcatgtattaattgcctgttgtttacttttttgcagAATTATCCGTGATATTATTCAAAATCATCTACTGCAA

- - - - - - - - -gcatact
- - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttg