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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaactaattttagaaaaatgggttgtctttcttttttaatattgttcaaaaacaacattcacctctacaatcttttcttcttcttgcctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAATGGAATGAACTTTATGGAGAAGGGGGTTCTAGAAGAAAGAAGGCTCTCA

Basic information

species Vitis vinifera
transcript Vv17s0000g01550.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA05G03270.2 (Glycine max), 3'ss of exon 23
gtaaaaaactaa-ttttagaaaaatgggttgtctttcttttttaatattgttcaaaaacaacattcacctctacaatcttttcttcttcttgcctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAATGGAATGAACTTTATGGAGAAGGGGGTTCTAGAAGAAAGAAGGCTCTCA
|||  |||  || ||| |   ||           | |  |  |   |    ||  |     | ||       | |   |  |       ||   | |||  |||| || || || ||||| || || |||||||| |||||||||||  |||||||||||||| | ||||||||||||||||| |||  |||||| || ||||
gtatgaaatgaaatttcatttaagcaaagccctctccagtcctttgagctctccgacttttcgtttttagtaatatgttacttcgtacattatattgaatcagGTATGTGCAAGTGTTTCTTCTGAATCAGTAAATATGACTGAGCTTTTACAATGGAATGAATTATATGGAGAAGGGGGTTCAAGAGTAAAGAAAGCACTCA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 25
gtaaaaaactaa-ttttagaaaaatgggttgtctttcttttttaatattgttcaaaaacaacattcacctctacaatcttttcttcttcttgcctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAATGGAATGAACTTTATGGAGAAGGGGGTTCTAGAAGAAAGAAGGCTCTCA
|||  |||  || ||| |   ||  |       || |  |      | |  ||  |    |  ||       | |   |  | |     ||   | |||  |||| || || || ||||| || ||||||||||| |||||||||||  | |||||||||||| | ||||||||||||||||| |||  |||||| || ||||
gtaggaaatgaaatttcatttaagcgaagccctttccaatcccttgagttctcccactttaggtttttagtaatatgttactttgtacattatattgaatcagGTATGTGCAAGTGTTTCTTCTGAGTCAGTAAATATGACTGAGCTTTTGCAATGGAATGAATTATATGGAGAAGGGGGTTCAAGAGTAAAGAAAGCACTCA
















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|71879230|gb|DT028285.1|DT028285
EST:     CTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|110394489|gb|EC959525.1|EC959525
EST:     CTGATATTCGACCTCTAAACATAGATGACTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTGATATTCGACCTCTAAACATAGATGACTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|110420390|gb|EC986662.1|EC986662
EST:     CTGATATTCGACCTCTAAACATAGATGACTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTGATATTCGACCTCTAAACATAGATGACTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|71878737|gb|DT027792.1|DT027792
EST:     CTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|71880061|gb|DT029116.1|DT029116
EST:     CTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|71879760|gb|DT028815.1|DT028815
EST:     CTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|71878454|gb|DT027509.1|DT027509
EST:     CTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
EST: gi|71877686|gb|DT026741.1|DT026741
EST:     CTTTAAATATGCTCATGAACGG                         GTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA
genomic: CTTTAAATATGCTCATGAACGGgtaaaaaact ... ctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcaaaaacaacattcacctctacaatcttttcttcttcttgcctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAATGGAATGAACTTTATGGAGAAGGGGGTTCTAGAAGAAAGAAGGCTCTCA
                   cctctacaatcttttc  CT-rich tract
     aaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaactaattttagaaaaatgggttgtctttcttttttaatattgttcaaaaacaacattcacctctacaatcttttcttcttcttgcctggaaatagGTTTGCGCTAGCGTTTCATCCGAGTCAGTAAACATGACTGAGCTAATACAATGGAATGAACTTTATGGAGAAGGGGGTTCTAGAAGAAAGAAGGCTCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG