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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctgcatttggtgctcttgagtcttgaccatatgactatactacttcaatcttcttttgtaaacatgttgtaaactaatttcttttttgggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAG

Basic information

species Vitis vinifera
transcript Vv09s0002g05250.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|71861182|gb|DT010237.1|DT010237
EST:     ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAG                         CTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGA
genomic: ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAGgtacatactt ... gggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGA
EST: gi|161714897|gb|FC064519.1|FC064519
EST:     ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAG                         CTGCGTCAGGAAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGA
genomic: ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAGgtacatactt ... gggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGA
EST: gi|110724133|gb|EE099692.1|EE099692
EST:     ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAG                         CTGCGTCAGGAAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGA
genomic: ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAGgtacatactt ... gggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGA
EST: gi|294965365|gb|GW837080.1|GW837080
EST:     ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAG                         CTGCGTCAGGAAAATAAGTTATATAAATCTT
genomic: ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAGgtacatactt ... gggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTT
EST: gi|26257746|gb|CA808809.1|CA808809
EST:     ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAG                         CTGCGTCAGGAAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGA
genomic: ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAGgtacatactt ... gggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGA
EST: gi|110394684|gb|EC959919.1|EC959919
EST:     ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAG                         CTGCGTCAGGAAAATAAGTTATATAATTCTTCAGTGATGGTTACTGCAGGA
genomic: ATGGTGCTGATGATGGTCTTCCTGAGCTCAGGGAGGCATTGGTAGAAAAGgtacatactt ... gggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaatcttcttttgtaaacatgttgtaaactaatttcttttttgggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAG
                             aactaat  putative branch site (score: 2)
                                   tttcttttttg  CT-rich tract
                        ttgtaaactaatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctgcatttggtgctcttgagtcttgaccatatgactatactacttcaatcttcttttgtaaacatgttgtaaactaatttcttttttgggtttgcagCTGCGTCAGGAAAATAAGTTATATAAATCTTCAGTGATGGTTACTGCAGGAGCAAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
catctgc
- - - - - - - gctcttg
- - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa