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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcacttcttaagcattttcagttgtgcaactctgatatggttttataaaaattgagtataaaatatgtcactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGATTGCACAGTTTGGATGTGGAATGCTGACAGAAGTGCCTACCTTAACATGT

Basic information

species Vitis vinifera
transcript Vv18s0164g00020.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0164g00020.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G31330.3 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------gtgcacttcttaagcattttcagttgtgcaactctgatatggttttataaaa-attgagt-ataaaatatgtcactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGATTGCACAGTTTGGATGTGGAATGCTGACAGAAGTGCCTACCTTAACATGT
                                                                                ||   |  |  ||   | |||| |    || |  | || |||||| |   | | ||| | |    |||  |   | |||||| | ||||||||||||||||||||  |  |||| |||||||| ||||||| ||   |||||||||||||| |||| |    |||||  ||||| |  |
gtgagattgttagtgaaaacaagttgttatttttgtagctattagtaaaagaaatatcaactggaaatgaaagcaataaacaaaacacacccacccttagttttcttgcttttttctgtttttattagttactaagttagatgccatgaaatctttcagTGGCTTAGGTGGCATCCAAGAGGACACATACTCTTAGCTGGTTCTGAGGATTTCAGCATTTGGATGTGGAATACTGATAATGCTGCCTTACTTAATACAT
















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|351035008|gb|FQ458365.1|FQ458365
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|351035588|gb|FQ463433.1|FQ463433
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAAGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|351024095|gb|FQ423518.1|FQ423518
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAAGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCA-AGGAA
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|351053931|gb|FQ441697.1|FQ441697
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAAGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|349826819|gb|FQ418910.1|FQ418910
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|351047151|gb|FQ454761.1|FQ454761
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|349830533|gb|FQ416810.1|FQ416810
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|352768135|gb|FQ467274.1|FQ467274
EST:     CTGCAGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCGTTGAG                         TGGGTCAGGTGGCATCCAAGAAGAGATTTGTTCTTGGCTGGTTCAG
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAG
EST: gi|351046079|gb|FQ441462.1|FQ441462
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
EST: gi|110722805|gb|EE099395.1|EE099395
EST:     CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAG                         TGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT
genomic: CTTCTGGAGACCTCAAGGGCACACTTGAAGGTCCTGGTGGAGGCATTGAGgtgcacttct ... cactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaactctgatatggttttataaaaattgagtataaaatatgtcactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGATTGCACAGTTTGGATGTGGAATGCTGACAGAAGTGCCTACCTTAACATGT
      ctctgat  putative branch site (score: 4)
         tgatatggttttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcacttcttaagcattttcagttgtgcaactctgatatggttttataaaaattgagtataaaatatgtcactgtgcagTGGGTCAGGTGGCATCCAAGAGGACATTTGGTCTTGGCTGGTTCAGAGGATTGCACAGTTTGGATGTGGAATGCTGACAGAAGTGCCTACCTTAACATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT