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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgatcacatgcattatgattccctttcagtccacatgtcacttttaagttaataactagaatggtcttcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTTGGAGAACAGAAAGTTGCCTCTATCGAGCAGCAACTCGCGTCATTGAATC

Basic information

species Vitis vinifera
transcript Vv14s0068g00720.t01
intron # 13
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|71861153|gb|DT010208.1|DT010208
EST:     TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
EST: gi|110381283|gb|EC946607.1|EC946607
EST:     AACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: AACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
EST: gi|161721331|gb|FC070058.1|FC070058
EST:     TTGCTAATGCTTCAGGCACTGAAAACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
EST: gi|110731966|gb|EE106841.1|EE106841
EST:     TTGCTAATGCTTCAGGCACTGAAAACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
EST: gi|30304038|gb|CB980832.1|CB980832
EST:     TTGCTAATGCTTCAGGCACTGAAAACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
EST: gi|71857364|gb|DT006419.1|DT006419
EST:     TTGCTAATGCTTCAGGCACTGAAAACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
EST: gi|30304101|gb|CB980895.1|CB980895
EST:     TTGCTAATGCTTCAGGCACTGAAAACAGCAGACAGAAAGAAGTACTCCAG                         GTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT
genomic: TTGCTAATGCTTCAGGCACTGAGAACAGCAGACAGAAAGAAGTACTCCAGgtgcttgatc ... tcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcagtccacatgtcacttttaagttaataactagaatggtcttcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTTGGAGAACAGAAAGTTGCCTCTATCGAGCAGCAACTCGCGTCATTGAATC
                           taataac  putative branch site (score: 1)
                                          tcttcgt  putative PPT
                   ttttaagttaataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttgatcacatgcattatgattccctttcagtccacatgtcacttttaagttaataactagaatggtcttcgtggtcagGTTGCCGTTACAGAAATTTTGGATGGTGGTAGATTCTATATCCAACCAGTTGGAGAACAGAAAGTTGCCTCTATCGAGCAGCAACTCGCGTCATTGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG