Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccaaactagaatttattggatctttcttctgttgggatgaatacttggcatgcattatgtaaattatctggttaatgggatgggttttgaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACAGTGCTTTATGAAG

Basic information

species Vitis vinifera
transcript Vv08s0040g00020.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|110374147|gb|EC938715.1|EC938715
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|27581758|gb|CB004453.1|CB004453
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|110726854|gb|EE103001.1|EE103001
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATT-ATATTGCTATTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|32245165|gb|CD710984.1|CD710984
EST:     CTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: CTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|27580823|gb|CB003518.1|CB003518
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|32250353|gb|CD716172.1|CD716172
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|161715399|gb|FC064896.1|FC064896
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|110368898|gb|EC933032.1|EC933032
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA
EST: gi|110701721|gb|EE079613.1|EE079613
EST:     TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAG                         GGTACATCTGTATT-ATATTGCTATTCACAGACTAAACATCAAATGGGACA
genomic: TTGTGGTGGTGCATTCACCTTCGGATTGATCAAATCCCTCCCCACCAAAGgtaattttgc ... gaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggcatgcattatgtaaattatctggttaatgggatgggttttgaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACAGTGCTTTATGAAG
                          ggttaat  putative branch site (score: 4)
          attatgtaaattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccaaactagaatttattggatctttcttctgttgggatgaatacttggcatgcattatgtaaattatctggttaatgggatgggttttgaaatttcagGGTACATCTGTATTCATATTGCTGTTCACAGACTAAACATCAAATGGGACAGTGCTTTATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- ccaaact
- - - - - - - - - - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - - - - - - - - -gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatggg