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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagcaccattttttaaagctgttctaaaaattgctttgcctagtaattttatttattggcttttcggtggctgatacaaaatacatttggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAAGAAACATGCAAGCAAAAGGAATCAAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04160.t01
intron # 9
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|219555116|gb|FG984377.1|FG984377
EST:     TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAG                         GAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
genomic: TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAGgtaaggttgc ... ggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
EST: gi|110403543|gb|EC969137.1|EC969137
EST:     TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAG                         GAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
genomic: TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAGgtaaggttgc ... ggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
EST: gi|219555059|gb|FG984848.1|FG984848
EST:     TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAG                         GAGTTACCTCCATAGACAAAACAGGCATAGAAACCCTGGTTGAAGTCCTAA
genomic: TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAGgtaaggttgc ... ggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
EST: gi|22011353|gb|BQ796387.1|BQ796387
EST:     TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAG                         GAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
genomic: TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAGgtaaggttgc ... ggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
EST: gi|219555052|gb|FG984841.1|FG984841
EST:     TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAG                         GAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA
genomic: TTCAAGTCCCAAAGGGACCAATGTCGAGCATGTGCTGCTAGATTTGGGAGgtaaggttgc ... ggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttatttattggcttttcggtggctgatacaaaatacatttggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAAGAAACATGCAAGCAAAAGGAATCAAG
                         ggctgat  putative branch site (score: 4)
 atacaaaatacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagcaccattttttaaagctgttctaaaaattgctttgcctagtaattttatttattggcttttcggtggctgatacaaaatacatttggctccacagGAGTTACCTCCATAGACATGACAGGCATAGAAACCCTGGTTGAAGTCCTAAGAAACATGCAAGCAAAAGGAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -agcacca
- - - - - - - - - - - - - taaaaat
- - - - - - - - - - - - - - - - - - - tgcctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaaa