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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCAATGGTCTTATCCAGAGAGTGCTGGCTGCATCTTATTCAGATATGGAAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttctaatgcctcaggattgataattttattaagatatctattttatccatattgctgtgtcacttgtatagagaacaggttttgtagaaaatatt...

Basic information

species Vitis vinifera
transcript Vv05s0020g00920.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00920.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G48280.1 (Arabidopsis thaliana), 5'ss of exon 3
CATCAATGGTCTTATCCAGAGAGTGCTGGCTGCATCTTATTCAGATATGGAAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttctaatgcctcaggattgataattttattaagatatctattttatccatatt--gctgtgtcacttgtata-------gagaacaggttttgtagaaaatatt------------------------------------------------------------------------------------
 ||||||| ||||||||||| ||| ||| |  | | || ||| |||||||||||  |  ||||||||||||||||||||||||| || ||  ||||  |||||| | ||||| ||||       ||  |||||   |  |  | | ||| |  | | |  ||  |||   | || ||       || |     |    || |||||||                                                                                     
TATCAATGATCTTATCCAGAAAGTTCTGACCACTTGTTTTTCGGATATGGAAGATGTCATGAAATTTGTGGATTGGCTTGATAAAGAACTGGCAACTCTGgtaactcctaattcctctttcaacatttttttacacaagtgacaagtttttgtaaactcggccatgtttttggtgtactgagacgaaagtgtatcacttataaaatatataaatgatcggttctccaaaatgagttttgcatcatacttatcttacattgtatgtgaattcctctttgcctattgccttacag
















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|351028554|gb|FQ444835.1|FQ444835
EST:     AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTG                         GCTGATGAGTGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
genomic: AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttcta ... cctttaatagGCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
EST: gi|351018677|gb|FQ424784.1|FQ424784
EST:     AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTG                         GCTGATGAGAGGGCTGTGCTAAAGCATTTCCAGTGGCCTGAGAAGAAAGCT
genomic: AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttcta ... cctttaatagGCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
EST: gi|351025939|gb|FQ427951.1|FQ427951
EST:     AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTG                         GCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
genomic: AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttcta ... cctttaatagGCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
EST: gi|110419624|gb|EC985867.1|EC985867
EST:     TGATAATGAGCTCTCAACCTTG                         GCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
genomic: TGATAATGAGCTCTCAACCTTGgtaatttcta ... cctttaatagGCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
EST: gi|351017822|gb|FQ436175.1|FQ436175
EST:     ACATTGTGAAAATTTGTGGATTGGCTTGATAAATGAACTCTTCAACCTTG                         GCTGATGAAAGGGCTGTGCTAAAGCATTTCAAGTTGGC-TGAGAAGAAAG
genomic: ACATTGTGAAA-TTTGTGGATTGGCTTGATAA-TGAGCTCT-CAACCTTGgtaatttcta ... cctttaatagGCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGT-GGCCTGAGAAGAAAG
EST: gi|349827883|gb|FQ422751.1|FQ422751
EST:     AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTG                         GCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT
genomic: AAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttcta ... cctttaatagGCTGATGAGAGGGCTGTGCTAAAGCATTTCAAGTGGCCTGAGAAGAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCAATGGTCTTATCCAGAGAGTGCTGGCTGCATCTTATTCAGATATGGAAGACATTGTGAAATTTGTGGATTGGCTTGATAATGAGCTCTCAACCTTGgtaatttctaatgcctcaggattgataattttattaagatatctattttatccatattgctgtgtcacttgtatagagaacaggttttgtagaaaatatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaata