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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaaaatattttctaaacactctacttttgctttatgtggatcaaagtttctgtttgctttttgcgtgaagtaactaactatgatcctctacacctgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTCAAGGAAAGTTTTTGGCAACAGAAAATTTCTTTTATACATCAAAG

Basic information

species Vitis vinifera
transcript Vv01s0026g02490.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G05750.1 (Glycine max), 3'ss of exon 5
gtttaaaatattttct-aaacactctactttt-gctttatgtggatcaaagtttctgtttgctttttgcgtgaagtaactaactatgatcctctacacctgaa--atgtagAGAGATGTTCATATCATCACTG---CTTAGGTTCAACTTTTATGCCCAAGCTTCAAGGAAAGTTTTTGGCAACAGAAAATTTCTTTTATACATCAAAG
|||||| || ||| | |||| || | || | | || || | || || || | ||| ||| | | | | | ||| ||| ||| |||||| ||||| ||||| | |||| |||||||| || || |||||||| || || |||||||| ||||||||||||||||| |||||||||
----gtcatatttactgaaattttgtactgttagattccctttaaaatgagattttcttcactgttgttttt--gtatttaagttggttatttcatgtttgatttatgcagAATCATGTTCCTATCAGCACTGTGACATAGGATCAACTTTCATACCAAAGCTTCAGGGGAAATTTTTGGCCACAGAAAATTTCTTTTACACATCAAAG

upper sequence: Vv01s0026g02490.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G11980.1 (Glycine max), 3'ss of exon 5
gtttaaaatattttcta-aacactctacttttgctttatgtggatca-aagtttctgtttgctttttgcgtgaagtaactaactatgatcctctacacctgaa--atgtagAGAGATGTTCATATCATCACTG---CTTAGGTTCAACTTTTATGCCCAAGCTTCAAGGAAAGTTTTTGGCAACAGAAAATTTCTTTTATACATCAAAG
|||||| ||| || | || | || ||| | | | || || | || || || | ||| ||| | | | | | ||| ||| ||| |||||| ||||| || || | |||| |||||||| || || |||||||| || || |||||||| || |||||||||||||| |||||||||
----gttatatttactacaattttgtattgttagattacctttaaaatgagattttcttcactgttgttttt--gtatttaagttggctatttcatgtttgatctatgcagAATCATGTTCCTATCAGCATTGTGACATAGGATCAACTTTCATACCAAAGCTTCAGGGGAAATTTTTGGCCACGGAAAATTTCTTTTACACATCAAAG
















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|71860764|gb|DT009819.1|DT009819
EST:     CTTCTCAGAATGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAG                         AGAGATGTTCATATCATCACTGCTTAGGTTCGACTTTTATGCCCAAGCTTC
genomic: CTTCTCAGAGTGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAGgtttaaaata ... tgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC
EST: gi|110356657|gb|EC919644.1|EC919644
EST:     CTTCTCAGAATGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAG                         AGAGATGTTCATATCATCACTGCTTAGGTTCGACTTTTATGCCCAAGCTTC
genomic: CTTCTCAGAGTGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAGgtttaaaata ... tgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC
EST: gi|30320456|gb|CD003718.1|CD003718
EST:     TTACAGAAGGGAAAAG                         AGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC
genomic: TTACAGAAGGGAAAAGgtttaaaata ... tgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC
EST: gi|110359018|gb|EC919806.1|EC919806
EST:     CTTCTCAGAATGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAG                         AGAGATGTTCATATCATCACTGCTTAGGTTCGACTTTTATGCCCAAGCTTC
genomic: CTTCTCAGAGTGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAGgtttaaaata ... tgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC
EST: gi|110357251|gb|EC920660.1|EC920660
EST:     CTTCTCAGAATGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAG                         AGAGATGTTCATATCATCACTGCTTAGGTTCGACTTTTATGCCCAAGCTTC
genomic: CTTCTCAGAGTGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAGgtttaaaata ... tgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC
EST: gi|110383715|gb|EC948106.1|EC948106
EST:     CTTCTCAGAATGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAG                         AGAGATGTTCATATCATCACTGCTTAGGTTCGACTTTTATGCCCAAGCTTC
genomic: CTTCTCAGAGTGTCGAGCTGCTGCATTAACCTTGTTACAGAAGGGAAAAGgtttaaaata ... tgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttgctttttgcgtgaagtaactaactatgatcctctacacctgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTCAAGGAAAGTTTTTGGCAACAGAAAATTTCTTTTATACATCAAAG
                      aactaac  putative branch site (score: 1)
 taactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaaaatattttctaaacactctacttttgctttatgtggatcaaagtttctgtttgctttttgcgtgaagtaactaactatgatcctctacacctgaaatgtagAGAGATGTTCATATCATCACTGCTTAGGTTCAACTTTTATGCCCAAGCTTCAAGGAAAGTTTTTGGCAACAGAAAATTTCTTTTATACATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA