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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcatcataacatgaactttatatagatcatagatgtgatttttggtggaataatgaaatacattttaaagttctgtaatacattaaaatactgcattcttatgtgtactaatttatttgataactcttgctggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTTTCAAATCGCTACCCAAATGCAAATTTATATGCTGTTGGTTGGTCTCTTG

Basic information

species Vitis vinifera
transcript Vv02s0025g02550.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02550.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S309_62V6.1 (Physcomitrella patens), 3'ss of exon 2
gtagcatcataacatgaactttatatagatcatagatgtgatttttggtggaataatgaaatacattttaaagttctgtaatacattaaaatactgcattcttatgtgtactaatttatttgataactcttgctggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTTTCAAATCGCTACCCAAATGCAAATTTATATGCTGTTGGTTGGTCTCTTG
   |  |  || |   | ||  |    | || |  || | || | |  |    |  |    |   ||||    || |  |||   |    |    | |   |||    || |  |||    || ||  ||   |    | ||||||||||| | ||||||||| ||||||||||| ||||| |||   || |   |       | ||||          | || ||||  || ||||||||||
---gttttctacctcaatctgcaagc-gttcgt--atttcatgtctctt---tttttttttttttttttttttttgtcaaatgtgtagctaggtagaaaattta---atagttttttgacagacaatgctctgttcgtttcagTTCTATTCCGGTTCATTTACCGAAGATTTGCGCCAAGTCGTGAAGCACGCCGCCTTCTTATTCCCATCCTTGCGAATCTACGCTGCAGGGTGGTCTCTTG
















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|28961249|gb|CB340635.1|CB340635
EST:     TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
EST: gi|38516575|gb|CF983750.1|CF983750
EST:     TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGANCACGGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
EST: gi|37186405|gb|CF605758.1|CF605758
EST:     TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
EST: gi|38516609|gb|CF983784.1|CF983784
EST:     TTGTGTTCAATAGCCGTGGCTGTGCGGATAGCCCCGTGACCACAGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
EST: gi|71866312|gb|DT015367.1|DT015367
EST:     TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
EST: gi|110372983|gb|EC937181.1|EC937181
EST:     TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
EST: gi|349825263|gb|FQ417984.1|FQ417984
EST:     TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAG                         TTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT
genomic: TTGTGTTCAATAGCCGTGGCTGTGCAGATAGCCCCGTGACCACGGCTCAGgtagcatcat ... tggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatactgcattcttatgtgtactaatttatttgataactcttgctggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTTTCAAATCGCTACCCAAATGCAAATTTATATGCTGTTGGTTGGTCTCTTG
                                      ctcttgct  CT-rich tract
                    tactaatttatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcatcataacatgaactttatatagatcatagatgtgatttttggtggaataatgaaatacattttaaagttctgtaatacattaaaatactgcattcttatgtgtactaatttatttgataactcttgctggaatgcagTTCTATTCAGCTTCATTTACAGAAGATTTGCGTCAAGTAGTGGCACATGTTTCAAATCGCTACCCAAATGCAAATTTATATGCTGTTGGTTGGTCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT