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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacaattatggtgtagaaaaaaattctgaattcaatagatcacatggtggtacataatctaatgatctgaggaagcctgttttttgttgatgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAAGAGATAGCAAAGAACTTGAAAAAGTACAGTAAGAAGTACGAGGCAGAGG

Basic information

species Vitis vinifera
transcript Vv04s0008g07070.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G27640.1 (Arabidopsis thaliana), 3'ss of exon 11
atacaattatggtgtagaaaaaaattctgaattcaatagatcacatggtggtacataatctaatgatctgaggaagcctgttttttgttgatgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAAGAGATAGCAAAGAACTTGAAAAAGTACAGTAAGAAGTACGAGGCAGAGG
       ||||    |  ||||| |   |   | ||  || ||        | |    |||||| |       |    ||| | | |||| | |  ||||||    ||||||||| |||| ||||| ||||||| | | ||||| || |||||||||||||||| | |||| |||||||| |||||||| ||||||||||
------gtatgtaacaagaaaaactc--ggtcttaaacgagcatcgtccattccgatgtctaataa------aatatttgtgtatggttggt-tacacagTTGGCTTGGCGTCCAAGACCTCCATCATTCTTGACTGCAGAGAAGGAAGAAGAGATAGCAAAGACCCTGAAGAAGTACAGCAAGAAGTATGAGGCAGAGG

upper sequence: Vv04s0008g07070.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G25780.1 (Arabidopsis thaliana), 3'ss of exon 10
atacaattatggtgtagaaaaaaattctgaattcaa-tag-atcacatggtggtacataatctaatgatctgaggaagcctgttttttgttgatgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAAGAGATAGCAAAGAACTTGAAAAAGTACAGTAAGAAGTACGAGGCAGAGG
       ||||    |  |||||| || |  |  || ||| ||||     |   | ||  |||||| |       |    ||| | | |||| | |  ||||||    ||||||||| ||||  |||| ||||||| | | ||||| || |||||||||||||||||| |||  || ||||| |||| ||| ||||||||||
------gtatgtaacaataaaaaactcggtctcaaactagcatcatccattttcagatg-tctaataa------aatatttgtgtatggttggt-tacacagTTGGCTTGGCGTCCAAGACCGGCATCATTCTTGACTGCGGAGAAGGAAGAAGAGATAGCAAAGAACCTGAGGAATTACAGCAAGAGGTATGAGGCAGAGG
















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|349828093|gb|FQ415421.1|FQ415421
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|351017906|gb|FQ439072.1|FQ439072
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|37183688|gb|CF603042.1|CF603042
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|71866867|gb|DT015922.1|DT015922
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCTGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|26267174|gb|CA818237.1|CA818237
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|351030721|gb|FQ438559.1|FQ438559
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|71868401|gb|DT017456.1|DT017456
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCTGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
EST: gi|351013418|gb|FQ425449.1|FQ425449
EST:     CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAG                         TTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA
genomic: CCTTCAACGGCAAGCTCCTGTATCGGATACTAAAGGATCACTTCTTCCAGgtaagatgaa ... atgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtggtacataatctaatgatctgaggaagcctgttttttgttgatgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAAGAGATAGCAAAGAACTTGAAAAAGTACAGTAAGAAGTACGAGGCAGAGG
         ataatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacaattatggtgtagaaaaaaattctgaattcaatagatcacatggtggtacataatctaatgatctgaggaagcctgttttttgttgatgtttacagTTCTTGTGGCGTCCACGACCACCATCCTTCTTGAGTCCCGAGAAAGAGGAAGAGATAGCAAAGAACTTGAAAAAGTACAGTAAGAAGTACGAGGCAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - -tggtgta
- - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - tcacatg