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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttgttggttttttttttttggttctagggttttgttttactagttgattatgggatgtgttggcgttgattttgatttttgatcgtttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATTTTGCGTAATTGGAGTGTTGGAAAATGGTGGAGGGTCCGAAATTCACTGG

Basic information

species Vitis vinifera
transcript Vv04s0008g03020.t01
intron # 1
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|110711504|gb|EE088057.1|EE088057
EST:     GAGAGAGAGCAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: GAGAGAGAGCAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|37187893|gb|CF607244.1|CF607244
EST:     CAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|26265228|gb|CA816291.1|CA816291
EST:     CAGCTCACGGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|110712948|gb|EE088439.1|EE088439
EST:     CAGCTCACAGCGTTGTCTACGGTCGG                     
genomic: CAGCTCACAGCGTTGTCTA----C-Ggtcgggtaac ... ttggtt
EST: gi|110720284|gb|EE096072.1|EE096072
EST:     GAGGAGAGAGAGAGCAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: GAGGAGAGAGAGAGCAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|110718302|gb|EE094983.1|EE094983
EST:     CAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|161718782|gb|FC066985.1|FC066985
EST:     AGAGAGCAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: AGAGAGCAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|71860537|gb|DT009592.1|DT009592
EST:     AGCTCACAGCGTTGTCTACGGTCGG                     
genomic: AGCTCACAGCGTTGTCTA----C-Ggtcgggtaac ... ttggtt
EST: gi|110699765|gb|EE077051.1|EE077051
EST:     CAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCTTATGCGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|110699069|gb|EE077287.1|EE077287
EST:     TCACAGCGTTGTCTACG                         GTTTGGTGGTGTCACATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: TCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|110685202|gb|EE063357.1|EE063357
EST:     CAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|71860395|gb|DT009450.1|DT009450
EST:     CTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
EST: gi|161721835|gb|FC071148.1|FC071148
EST:     CAGCTCACAGCGTTGTCTACG                         GTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT
genomic: CAGCTCACAGCGTTGTCTACGgtcgggtaac ... ttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgattatgggatgtgttggcgttgattttgatttttgatcgtttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATTTTGCGTAATTGGAGTGTTGGAAAATGGTGGAGGGTCCGAAATTCACTGG
                                   ttttgat  putative branch site (score: 4)
                        ttgattttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttgttggttttttttttttggttctagggttttgttttactagttgattatgggatgtgttggcgttgattttgatttttgatcgtttggttctagGTTTGGTGGCGTCAGATGAGCTTTGATTAATTCAATTTCTAGGGTTTTATTTTGCGTAATTGGAGTGTTGGAAAATGGTGGAGGGTCCGAAATTCACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - -tgttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgtg