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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgctttagaatctttcttgcctttttctaatcatattttatttttattaaatgcatatccttcatctataatgacattgatggttttgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG

Basic information

species Vitis vinifera
transcript Vv14s0060g02240.t01
intron # 4
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|37189618|gb|CF608967.1|CF608967
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGATGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCAG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|71866659|gb|DT015714.1|DT015714
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|37189144|gb|CF608493.1|CF608493
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCAG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|110368812|gb|EC932903.1|EC932903
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|71886236|gb|DT035291.1|DT035291
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|37184974|gb|CF604327.1|CF604327
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGATGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCAG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|110400007|gb|EC966544.1|EC966544
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
EST: gi|37189131|gb|CF608480.1|CF608480
EST:     AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAG                         GTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCAG
genomic: AATGCTACATTCGTGGGAATACAATTAAGTATCTCAGAGTCCCTGACGAGgtatatttgg ... tgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattaaatgcatatccttcatctataatgacattgatggttttgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG
                                 cattgat  putative branch site (score: 4)
                      atctataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgctttagaatctttcttgcctttttctaatcatattttatttttattaaatgcatatccttcatctataatgacattgatggttttgtgttccagGTGATTGATAAAGTTCAGGAAGAAACAAAAAATCGTGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
ttcttgc
- - - - - - - - - -cttgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatggt