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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG

Basic information

species Vitis vinifera
transcript Vv05s0020g03080.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
----aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
      | | | || | | | |      | |||| |   | ||    || |  |  |||||     | | |   |   || ||  |    ||| | | |||||||  | ||||| |||||||| || |||||||| ||||| ||||||||||| || ||||||||||| ||||| |||||| ||||  | |   | ||| | ||
ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttt-tgcgtgctatcacactctcata---atgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
------------------------------------aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgc-tgctctattttgggataaattt-----atgttaatt-tgtcc---tctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
                                     | ||  ||  |||  ||  ||   |||  ||||  ||  |  || | || | ||     | |   ||   | |   ||     | |  |||| |||     | |||||||  | || || |||||||| || |||||||| ||||| ||||||||| | || ||||||||||| |||||||||||| |||| || |   | ||    ||
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtc-cttttgttcacagtaattc-ctcactgttattgtttttgtacattatcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
-aacaagaaaaatgtggctcctgagtacaacaat-tttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
 | |||   | ||     |||  | ||      | |  ||||    | | || | |  ||    | ||| | | |  |  || ||  | | |||  ||||||| ||||| ||||||||||| || |||||||| || |||||||| ||||| || ||||||||||| ||||| |||||| | || || ||  | || |  ||
aatcaaatgacatccatatccaaaataattgggtgtgcctttgtgcttttgtat-tattgtcacagtttcgta-atgtggatctttgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 16
aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttat-gttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
 ||     |     |  |    |  |  | | || | |||   || ||   | ||  ||| | || ||          |  |||   || |  | |||||||  | || |||||||||||||| ||||||||||| |||||||| ||||||||| |||| ||||||||||| |||||  ||||||||||| ||||||  ||
cactttttatggaagaatttaaaagatga-agttatatttaatttatgtcatctgtagctttcttatgcctagtgccaagagttttgttcttttgtttcagAGATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCATTGTTTTTCGGGG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttat-gttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
  |     |     |  |    |  |  | |||| | |||   || ||     ||  ||| | || ||          |  |||   || |  | |||||||  | || || ||||||||||| ||||||||||| |||||||| ||||||||| |||| ||||||||||| |||||  |||||||| || |||||| |||
ctccttttatgaaagaatttaaaagatga-aattatgtttaatttatgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G34650.1 (Glycine max), 3'ss of exon 4
------------------aacaag--aaaaatgtggctcctgagtacaacaat---tttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAA---GCTTGTGGATGTTCCGGAA--ATGAACTACACATCTGAGGAT--CAGCCCTAT----CCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG-------------------------
                  || |||   | |    |  | |    ||   || |   |  ||  |  || |   | |   |  |  | ||| ||| | ||||   ||  || |||   |  | ||||   |     |   |||   ||  |    || |  | ||    |||||||  || || | |     ||| |  || |  ||||| |      |   |   | ||| ||                          
gttttcaacaagataaaaaagaagcttagaggacgagttcgagttatggcattaggtgcctcacatttatcacccgatttcatggaattttgga-agatttgccttggtt-gtcggatgactgaaggatatgcaatgacggagagtcttgtgttataagTTGCATTGATGAGGATGACAACCTTGTTGGCTCTCCTAATGTAGCCTGTGATATAAAACTTGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
--------aacaagaaaaatgtggc-tcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
           |   |   || |   |  | |||| |  |||||       | | |   |  |  |    |  ||||||||   || || |  |||| |  | |||||||||| |||||||||||||| || ||||||||||| ||||| | |||||||||| |||| ||||| ||||| |||||| ||||||| ||  |||||  |||
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatat---ccattttaaattgctttgggat---ttaatatgcatttcta-tatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG

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|71889597|gb|DT038652.1|DT038652
EST:     GGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: GGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|110414986|gb|EC980854.1|EC980854
EST:     TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACAGATCTGAGGATCAGC
genomic: TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|46917646|gb|CN546975.1|CN546975
EST:     TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|71882993|gb|DT032048.1|DT032048
EST:     GGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: GGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|161720583|gb|FC069911.1|FC069911
EST:     TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|46917526|gb|CN546855.1|CN546855
EST:     TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|71881187|gb|DT030242.1|DT030242
EST:     GGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: GGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|161720400|gb|FC069849.1|FC069849
EST:     TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: TGAGAGTGACAACCTAACCGGTCATGTTGGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
EST: gi|71882474|gb|DT031529.1|DT031529
EST:     GGATCACCTAATCCAGCTTGTG                         AAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC
genomic: GGATCACCTAATCCAGCTTGTGgtgagtcatc ... cctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG
                                  tgttaat  putative branch site (score: 3)
                                        tttgtcctctttc  CT-rich tract
                tattttgggataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttatgttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG

- -aagaaaa
- - - - - - - - ctcctga
- - - - - - - - - - - - -acaacaa
- - - - - - - - - - - - - - - - - -tctttcc
- - - - - - - - - - - - - - - - - - - - - - - - -tctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggataaa