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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgaatttcaccacctgtctcttttatgtattaactctaaatattggaggcaatgaagtgtcttgtacttattaactatccttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATATGGCTGAGCAGCTTGCTATG

Basic information

species Vitis vinifera
transcript Vv07s0005g04440.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04440.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G18950.1 (Glycine max), 3'ss of exon 5
-----------gtattg-aatttcaccacctgtctctttta-tgtattaactctaaatattggaggcaatgaagtgtcttgtacttattaact-atcc--ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATATGGCTGAGCAGCTTGCTATG
           || ||| ||||| ||    ||  | ||| | | | || |     |  | |    |   |  | |  |     | |  |  || ||    |||| |||||||||||| |||||||||||||| || |||||||| |||||| || |||| ||||||||||| || || | |
gtatacatcttgtcttgtaattttacgctttgaatgtttcaatatgttgaagtatacgactctttgtgtttcaatcacacactcattctgccttatttggttgttggcagGAAGGGATTATGAGACAAGAAACTACAGCTTTGAAGAAGTGCACTATCACATGGCTGAGCAACTAGCAAAG
















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|161719785|gb|FC066692.1|FC066692
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
EST: gi|161720302|gb|FC071155.1|FC071155
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
EST: gi|161719288|gb|FC068264.1|FC068264
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
EST: gi|77580795|gb|DV219305.1|DV219305
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
EST: gi|110424142|gb|EC990498.1|EC990498
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
EST: gi|71864241|gb|DT013296.1|DT013296
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGTACCATC
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATC
EST: gi|161718481|gb|FC066331.1|FC066331
EST:     TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTG                         GAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA
genomic: TTCGATCAAGGCAGTAATGGCGAAAGCTAACGTTGTTCTCAATCTTATTGgtattgaatt ... ttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaatattggaggcaatgaagtgtcttgtacttattaactatccttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATATGGCTGAGCAGCTTGCTATG
                                 tattaac  putative branch site (score: 1)
                                       ctatcctt  CT-rich tract
                             tacttattaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgaatttcaccacctgtctcttttatgtattaactctaaatattggaggcaatgaagtgtcttgtacttattaactatccttgtgggcagGAAGGGAATATGAGACAAGAAATTATAGCTTTGAGGAAGTGAACCATCATATGGCTGAGCAGCTTGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT