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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttttttcatctcaattgtcttttaacttttgtatagttaatgctctgtttggttggtgagaaagtgtgggaaaagcaacgtaaatcggaatacggtttctcgttaacctggcgtaccttaactgtttctaatttgtaatttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATCACATTTAAAGCTCTTAAG

Basic information

species Vitis vinifera
transcript Vv18s0072g00460.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|110690720|gb|EE068124.1|EE068124
EST:     AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAG                         TTAGAGGATTCTCTGGTTGATTTGCTTCAAAGTCTCGCAGACATGGATATC
genomic: AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAGgttttttttt ... atttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
EST: gi|110718406|gb|EE095199.1|EE095199
EST:     AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAG                         TTAAAGGAATCTCTGGTTGATTTGCTTCAAAGTCTCGCAGACCTGGATATC
genomic: AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAGgttttttttt ... atttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
EST: gi|156736039|gb|EV240153.1|EV240153
EST:     AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAG                         TTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
genomic: AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAGgttttttttt ... atttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
EST: gi|34548933|gb|CF517165.1|CF517165
EST:     AGCAGTCTAAGATTCTTGCGATCAAGGAGCACCTTGAAGATCCTGATCAG                         TTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
genomic: AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAGgttttttttt ... atttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
EST: gi|34548840|gb|CF517072.1|CF517072
EST:     AGCAGTCTAAGATTCTTGCGATCAAGGAGCACCTTGAAGATCCTGATCAG                         TTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
genomic: AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAGgttttttttt ... atttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
EST: gi|33407190|gb|CF212817.1|CF212817
EST:     AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAG                         TTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC
genomic: AGCAGTCTAAGATTCTTGCGATCAAGGAGCGCCTTGAAGATCCTGATCAGgttttttttt ... atttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtttctcgttaacctggcgtaccttaactgtttctaatttgtaatttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATCACATTTAAAGCTCTTAAG
                                 ttctaat  putative branch site (score: 2)
                                              tttcttc  putative PPT
                                tttctaatttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttttttcatctcaattgtcttttaacttttgtatagttaatgctctgtttggttggtgagaaagtgtgggaaaagcaacgtaaatcggaatacggtttctcgttaacctggcgtaccttaactgtttctaatttgtaatttcttcagTTAGAGGATTCTCTGGTTGATTTGCTTCAGAGTCTCGCAGACATGGATATCACATTTAAAGCTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA