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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataccatttttccaatctttcgatttccgtctatttatattcccatgctctctcatttttttttttttaaaaaaaaaaaaaaatctattttccctgcaaccaaccgacggttagggttttcagtctttaactctatttacattctctgcatcacagAAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCCGAGGGTCCTGTGCTCAAGCGCAGCTATGGCAATGAAGAAATTAGCATTT

Basic information

species Vitis vinifera
transcript Vv13s0073g00620.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|161715678|gb|FC067796.1|FC067796
EST:     GCTCCCTCAGAGACCACTATCTCGAAGTTTCCAAAATGACTCCTCCTCCG                         AAGGTGAGCCCTCCATCTCCATTCTCCATCATCAAAGGTGCGCTCGACTCC
genomic: GCTCCCTCAGAGACCACTATCTCGAAGTTTCCAAAATGACTCCTCCTCCGgtataccatt ... tgcatcacagAAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCC
EST: gi|110407570|gb|EC973172.1|EC973172
EST:     GCTCCCTCAGAGACCACTATCTCGAAGTTTCCAAAATGACTCCTCCTCCG                         AAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCC
genomic: GCTCCCTCAGAGACCACTATCTCGAAGTTTCCAAAATGACTCCTCCTCCGgtataccatt ... tgcatcacagAAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCC
EST: gi|110373060|gb|EC937267.1|EC937267
EST:     GCTCCCTCAGAGACCACTATCTCGAAGTTTCCAAAATGACTCCTCCTCCG                         AAGGTGAGCCCTCCATCTCCATTCTCCATCATCAAAGGTGCGCTCGACTCC
genomic: GCTCCCTCAGAGACCACTATCTCGAAGTTTCCAAAATGACTCCTCCTCCGgtataccatt ... tgcatcacagAAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccgacggttagggttttcagtctttaactctatttacattctctgcatcacagAAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCCGAGGGTCCTGTGCTCAAGCGCAGCTATGGCAATGAAGAAATTAGCATTT
                       ctttaac  putative branch site (score: 3)
                                      cattctct  putative PPT
                        tttaactctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataccatttttccaatctttcgatttccgtctatttatattcccatgctctctcatttttttttttttaaaaaaaaaaaaaaatctattttccctgcaaccaaccgacggttagggttttcagtctttaactctatttacattctctgcatcacagAAGGTGAGCCCTCCATCTCCATTCTCCATTATCAAAGGTGCGCTCGACTCCGAGGGTCCTGTGCTCAAGCGCAGCTATGGCAATGAAGAAATTAGCATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA