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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcctaagtgggttattttatattaaataagcctttttcccttttcaatttatccatcacaagaagttctgttcactaaattttctctacgtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTTGATCAGCACAGAGAGATGAGACTGGATGTAGACAATATGAGCTATGAG

Basic information

species Vitis vinifera
transcript Vv08s0040g02160.t01
intron # 3
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|110386709|gb|EC951326.1|EC951326
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|71890758|gb|DT039813.1|DT039813
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|110698522|gb|EE076116.1|EE076116
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|71880900|gb|DT029955.1|DT029955
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|110360203|gb|EC922989.1|EC922989
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|110359745|gb|EC921816.1|EC921816
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|110359702|gb|EC921626.1|EC921626
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|110359655|gb|EC921489.1|EC921489
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|22015326|gb|BQ800360.1|BQ800360
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|110358811|gb|EC923300.1|EC923300
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|77583866|gb|DV220970.1|DV220970
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|77578962|gb|DV218312.1|DV218312
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
EST: gi|71879182|gb|DT028237.1|DT028237
EST:     TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAG                         GGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT
genomic: TCCGATCACTCTCTGATGAGGCAGGTGTCCGTGAGCGACTGGCATCTGAGgtttgttatc ... gtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttatccatcacaagaagttctgttcactaaattttctctacgtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTTGATCAGCACAGAGAGATGAGACTGGATGTAGACAATATGAGCTATGAG
                            cactaaa  putative branch site (score: 2)
                                   ttttctctacgtcttt  CT-rich tract
                             actaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcctaagtgggttattttatattaaataagcctttttcccttttcaatttatccatcacaagaagttctgttcactaaattttctctacgtctttgcagGGACTAATGATTGTGGATCGCTCAGCCTTGTATGGGTCAAGAAATTTGTTTGATCAGCACAGAGAGATGAGACTGGATGTAGACAATATGAGCTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - -gtgggtt
- - - - - - - - - - - - aaataag
- - - - - - - - - - - - - - - - - - - ccctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactaaa