Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgaagaacaaataatccaatttagtacttcatttttacttcttccctcgtggctaaacatgcttgcagtggactaacaaaatttttctgctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCACACTCTGCAAAGCTTTGTATATTACTGAGGATAATAAAGGGGTTCTAAAA

Basic information

species Vitis vinifera
transcript Vv01s0011g00600.t01
intron # 11
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|32460112|gb|CD801286.1|CD801286
EST:     GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
EST: gi|34362742|gb|CF404327.1|CF404327
EST:     GTGTTCCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
EST: gi|71884544|gb|DT033599.1|DT033599
EST:     GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
EST: gi|34362625|gb|CF404210.1|CF404210
EST:     GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
EST: gi|110365764|gb|EC929197.1|EC929197
EST:     GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
EST: gi|34363556|gb|CF405141.1|CF405141
EST:     GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
EST: gi|22012480|gb|BQ797514.1|BQ797514
EST:     GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGG                         AAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC
genomic: GTGTTGCCATTTACTCCCTCATAAAGGCAAACATTGAAGAGCAAAAACGGgtaagatttt ... gctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctcgtggctaaacatgcttgcagtggactaacaaaatttttctgctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCACACTCTGCAAAGCTTTGTATATTACTGAGGATAATAAAGGGGTTCTAAAA
                           gactaac  putative branch site (score: 1)
                                      tttttctgctacttc  putative PPT
                            actaacaaaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgaagaacaaataatccaatttagtacttcatttttacttcttccctcgtggctaaacatgcttgcagtggactaacaaaatttttctgctacttcagAAAGCTGCTGTAACTCCAGCATCATAGAGCTATCGAATCTATCCTACCCACACTCTGCAAAGCTTTGTATATTACTGAGGATAATAAAGGGGTTCTAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- -gaagaac
- - - - - - - aatccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa