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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccagctttcagcaaatatcttcttttgattcccaccagaagttataaacctttagctcaatcagtaatttaggctcctttctgttttttctgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATCCATGGCCAAAATCAATCCCCCTTTTGATAGAGAAAGCATAAGAGGAATA

Basic information

species Vitis vinifera
transcript Vv04s0008g03730.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G08700.1 (Glycine max), 3'ss of exon 3
ccagctttcagcaaatatcttcttttgattcccaccagaagttataa--acctttagctcaatcagtaatttaggctcctttctgtttt-ttctgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATCCATGGCCAAAATCAATCCCCCTTTTGATAGAGAAAGCATAAGAGGAATA
  |   |  |     ||| |||     |||      |||| || | |  |  ||| |   | |   |||  |         | | |||| | |  | |   ||||| ||||| ||| |||| || ||||| ||||| ||| |||||||||||||||  |||||||| || ||||| | |||| | | || |||||||||||||
--aaaataaaatttttatgttcaaccaattga-gttagaattttttattattttttgtatattttttaagctgtcaaatgatgtattttatgcattattatagATACCTCTACGAGCTGGATCAACACCTTGACCGCTTTATAAGGTCAGCATCCACAGCCAAAATAAACCCCCCATATGATCGTGGAACCATAAGAGGAATA

upper sequence: Vv04s0008g03730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G26230.2 (Glycine max), 3'ss of exon 2
ccagctttcagcaaatatcttcttttgattcccaccaga-agttataaacctttagctcaatcagtaatttag----gctcctttctgttttttctgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATCCATGGCCAAAATCAATCCCCCTTTTGATAGAGAAAGCATAAGAGGAATA
   ||    |  |   ||       |||||  ||||  | | | |  |  |||| | |   || |   ||||     |     |  ||| |||| ||  |   ||||| || |||||| | || || ||||| || || ||| ||||||||||||||||| | |||||  ||||||| |||||| ||| |||||||||| |||||
---gcagcaataatggatgggtcagtgattttcacctcataataactactcttttgttt--tctgccttttaaagcagtcaaatgatgtattttgtgcattatagATACCTATATGAGCTAGATCAACACCTTGATCGCTTTTTAAGGTCAGCATCCATGTCTAAAATAGATCCCCCATTTGATCGAGGAAGCATAAGAAGAATA

upper sequence: Vv04s0008g03730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G26230.1 (Glycine max), 3'ss of exon 3
ccagctttcagcaaatatcttcttttgattcccac-cagaagttataaacctttagctcaatcagtaatttaggctcctttctgttttttctgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATCCATGGCCAAAATCAATCCCCCTTTTGATAGAGAAAGCATAAGAGGAATA
       ||||  | | ||  ||  | ||  | || |    ||| |   |||||   | || |||| |  |           ||| |||| ||  |   ||||| || |||||| | || || ||||| || || ||| ||||||||||||||||| | |||||  ||||||| |||||| ||| |||||||||| |||||
------gtcagtgattttcacctcataataactactcttttgttttctgccttt---taaagcagtcaaatga---------tgtattttgtgcattatagATACCTATATGAGCTAGATCAACACCTTGATCGCTTTTTAAGGTCAGCATCCATGTCTAAAATAGATCCCCCATTTGATCGAGGAAGCATAAGAAGAATA

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|161710053|gb|FC060245.1|FC060245
EST:     ATGGTCCATCGAGGTCACGGAGTCTTTGATACTGCAGCAATAATGGATGG                         ATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATC
genomic: ATGGTCCATCGAGGTCACGGAGTCTTTGATACTGCAGCAATAATGGATGGgttagtgatt ... tgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATC
EST: gi|71855581|gb|DT004636.1|DT004636
EST:     ATGGTCCATCGAGGTCACGGAGTCTTTGATACTGCAGCAATAATGGATGG                         ATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCT
genomic: ATGGTCCATCGAGGTCACGGAGTCTTTGATACTGCAGCAATAATGGATGGgttagtgatt ... tgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCT
EST: gi|161715879|gb|FC065498.1|FC065498
EST:     ATGGTCCATCGAGGTCACGGAGTCTTTGATACTGCAGCAATAATGGATGG                         ATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATC
genomic: ATGGTCCATCGAGGTCACGGAGTCTTTGATACTGCAGCAATAATGGATGGgttagtgatt ... tgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacctttagctcaatcagtaatttaggctcctttctgttttttctgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATCCATGGCCAAAATCAATCCCCCTTTTGATAGAGAAAGCATAAGAGGAATA
                            ctcctttctgtttttt  CT-rich tract
                 agtaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccagctttcagcaaatatcttcttttgattcccaccagaagttataaacctttagctcaatcagtaatttaggctcctttctgttttttctgtgtcccagATATCTCTATGAGTTGGACCAGCACCTAGACCGTTTTCTAAGGTCAGCATCCATGGCCAAAATCAATCCCCCTTTTGATAGAGAAAGCATAAGAGGAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
ccagctt
- - - -tcagcaa
- - - - - - - - - - - - - - - cccacca
- - - - - - - - - - - - - - - - - - - - - -ataaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaatca