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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgctttttaactccatgtgcctgtcattgtactgagatttttccaggataccgacacattattttgtagattaattctgataccagtgttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGCAGTTTCTGGCCTGCAAATGGCAACAGCAAGGTCCCATATTTCTTCCTCT

Basic information

species Vitis vinifera
transcript Vv06s0004g01310.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|351029554|gb|FQ427394.1|FQ427394
EST:     AATTACTTCCCCCTGTTTTCATATCACAGCGGAGTTTTCCATCCCAATAG                         ATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCTGAAAATGGCAGCAACTGC
genomic: AATTACTTTCCCCTGTTTTCATATCACAGCGAAGTTTTCCATCCCAATAGgtaattttgt ... ttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGC
EST: gi|349827600|gb|FQ422468.1|FQ422468
EST:     AATTACTTTCCCCTGTTTTCATATCACAGCGGAGTTTTCCATCCCAATAG                         ATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCTGAAAATGGCAGCAACTGC
genomic: AATTACTTTCCCCTGTTTTCATATCACAGCGAAGTTTTCCATCCCAATAGgtaattttgt ... ttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGC
EST: gi|351014663|gb|FQ437665.1|FQ437665
EST:     AATTACTTTCCCCTGTTTTCATATCACAGCGGAGTTTTCCATCCCAATAG                         ATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCTGAAAATGGCAGCAACTGC
genomic: AATTACTTTCCCCTGTTTTCATATCACAGCGAAGTTTTCCATCCCAATAGgtaattttgt ... ttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGC
EST: gi|71854871|gb|DT003926.1|DT003926
EST:     AATTACTTTCCCCTGTTTTCATATCACAGCGGAGTTTTCCATCCCAATAG                         ATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCTGAAAATGGCAGCAACTGC
genomic: AATTACTTTCCCCTGTTTTCATATCACAGCGAAGTTTTCCATCCCAATAGgtaattttgt ... ttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGC
EST: gi|349828693|gb|FQ418428.1|FQ418428
EST:     AATTACTTTCCCCTGTTTTCATATCACAGCGGAGTTTTCCATCCCAATAG                         ATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCTGAAAATGGCAGCAACTGC
genomic: AATTACTTTCCCCTGTTTTCATATCACAGCGAAGTTTTCCATCCCAATAGgtaattttgt ... ttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGC
EST: gi|351043798|gb|FQ431350.1|FQ431350
EST:     AATTACTTCCCCCTGTTTTCATATCACAGCGGAGTTTTCCATCCCAATAG                         ATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCTGAAAATGGCAGCAACTGC
genomic: AATTACTTTCCCCTGTTTTCATATCACAGCGAAGTTTTCCATCCCAATAGgtaattttgt ... ttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggataccgacacattattttgtagattaattctgataccagtgttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGCAGTTTCTGGCCTGCAAATGGCAACAGCAAGGTCCCATATTTCTTCCTCT
                               ttctgat  putative branch site (score: 3)
                                           tgttctctcc  putative PPT
            acattattttgtagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgctttttaactccatgtgcctgtcattgtactgagatttttccaggataccgacacattattttgtagattaattctgataccagtgttctctccagATTTCTGTTTTCCTCTGCAAGATTCAAGTTGCCGAAAATGGCAGCAACTGCAGTTTCTGGCCTGCAAATGGCAACAGCAAGGTCCCATATTTCTTCCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
-ctgcttt
- - - - - - ctccatg
- - - - - - - - - - -cctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - ccgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatacc