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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaacattaaactgatccattctagcattgtctcctcatttccacaatcttaggtatttgcatctcagatgctaatgtatttgctgtttcccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAGCTTATATGTGGCTAGATGCTGAGCTGACATCTGGATCTGGAAGTAATGT

Basic information

species Vitis vinifera
transcript Vv18s0001g11820.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os03g42820.3 (Oryza sativa), 3'ss of exon 13
------------------------------ggaaacattaaactgatccattctagcattgtctcctcatttccac-aatcttaggtat-ttgcatctcagatgctaatgtatttgctgtttcccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAGCTTATATGTGGCTAGATGCTGAGCTGACATCTGGATCTGGAAGTAATGT
                               |  | ||  |      ||  | | |  |    |   | ||      ||  |||| | | ||| || | | ||  | |  | ||           |||  ||| || | ||||||||  | | | || |||||||| ||||||||||| |||||| |||||||||| ||  | ||  | ||||| |||||| | || |   |
gtactacagttacccttttttaccttttgcagctatatctattcatacctctgtggattaacgtaggctttcatgttaaatttagttctattgaatgttacat--ttacatcttaataacaatttttgtcagGATACCAAACTCTTGATCCAAAGGTCGAAGAAGGCATCTGTCAGGTTCTAGCTCATATGTGGCTCGAGTCAGAAATAACATCAGGATCTAGTAGCATCAT

upper sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G36620.1 (Glycine max), 3'ss of exon 10
----------------ggaaac--attaaactg--atccattctagcattgtctcctcatttcca-----caatcttaggtatttgcatctcagatgctaatgtatttgctgtttcccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAGCTTATATGTGGCTAGATGCTGAGCTGACATCTGGATCTGGAAGTAATGT
                |||||   |||    |   || |||| ||||| |   |  | ||  ||       || |  | ||   | | |      ||    |  | ||  || |  | |  ||||||||||| |||||    |||||||| ||||||||||||||||||||  | ||| |||||||| | ||  |||| ||  | |||| ||| || || ||  |
gtactattttatcataggaaatttatttcgttagaattcattttagcagttgatatttatgacctactgttaaaccaatgttagttcgttgggattgtctctcaaatttatgctaacttgtgaagGTTATCGGACTCTAAGTCAAGATGTTGAAGAAGGTATCTGTCAGGTTTTGGCTCATATGTGGTTGGAATCTGAACTTTCTTCTGCATCAGGCAGCAACTT

upper sequence: Vv18s0001g11820.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G08450.1 (Glycine max), 3'ss of exon 11
-----------------ggaaac-attaaact--gatccattctagcatt---gtctcctcatttcca--caatcttaggtatttgcatctcagatgctaatgtatttgctgtttcccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAGCTTATATGTGGCTAGATGCTGAGCTGACATCTGGATCTGGAAGTAATGT
                 |||| | |||  | |  ||| |||| ||||| |   |  |  |||  | |    || |    ||  || | |      ||    |  | ||  || |  | |  ||||||||||| |||||    |||||||| ||||||||||||||||||||  |  || |||||||| | ||  |||| ||  | |||| ||| || || ||  |
gtactattttattgttgggaatctatttcattaggattcattttagcagttgagatttatcacctactattaaaccagtgttatttcgttgggattgtctctcaaattcatgctaacttgtgaagGTTATCGGACTCTAAGTCAAGATGTTGAAGAAGGTATCTGTCAGGTTTTGTCTCATATGTGGTTGGAGTCTGAACTTTCTTCTGCATCAGGCAGCAACTT

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|33407704|gb|CF213331.1|CF213331
EST:     TGGGTCGATTCTTGCTCACGAGATGATGCATGCCTGGCTCCGACTAAATG                         GTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAG
genomic: TGGGTCGATCCTTGCTCACGAGATGATGCATGCCTGGCTCCGACTAAATGgtgctccact ... cccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcttaggtatttgcatctcagatgctaatgtatttgctgtttcccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAGCTTATATGTGGCTAGATGCTGAGCTGACATCTGGATCTGGAAGTAATGT
                         tgctaat  putative branch site (score: 2)
                                   tttgctgtttccctt  putative PPT
                            taatgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaacattaaactgatccattctagcattgtctcctcatttccacaatcttaggtatttgcatctcagatgctaatgtatttgctgtttcccttggaagGTTATCGAACTCTTGCACAAGATGTGGAAGAAGGTATCTGTCAGGTGCTAGCTTATATGTGGCTAGATGCTGAGCTGACATCTGGATCTGGAAGTAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
ggaaaca
- - - - -aaactga
- - - - - - - - -ccattct
- - - - - - - - - - - - - - - -tctcctc
- - - - - - - - - - - - - - - - - - - - -tccacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt