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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttcaagtacagatatttacatgttactcacaaagttgatgtttagtgaaagttgaaactgtggttgatgaaaacaaaatgttggttaccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG

Basic information

species Vitis vinifera
transcript Vv12s0142g00360.t01
intron # 6
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|110728991|gb|EE105103.1|EE105103
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|110726323|gb|EE102002.1|EE102002
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|110715529|gb|EE093682.1|EE093682
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|110730325|gb|EE107273.1|EE107273
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|30298144|gb|CB974938.1|CB974938
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAGGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|30135782|gb|CB921120.1|CB921120
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTACATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|110710338|gb|EE086596.1|EE086596
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|30133145|gb|CB918484.1|CB918484
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTACATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|30298778|gb|CB975572.1|CB975572
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
EST: gi|110726263|gb|EE101892.1|EE101892
EST:     AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGG                         GAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
genomic: AATGAATTGCTGTTTGCTGAAATCGAGTATATGCAAAAGAGGgtaaataatg ... ccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgaaagttgaaactgtggttgatgaaaacaaaatgttggttaccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG
                   ggttgat  putative branch site (score: 5)
                                          ttacctt  putative PPT
                           aaaacaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttcaagtacagatatttacatgttactcacaaagttgatgtttagtgaaagttgaaactgtggttgatgaaaacaaaatgttggttaccttgtgcagGAGATTGAGCTCCAAAACAGTAACTTATTTCTGCGAGCACAG

- - tcaagta
- - - - - - - - - - acatgtt
- - - - - - - - - - - - - - ctcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggt