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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG

Basic information

species Vitis vinifera
transcript Vv00s0568g00010.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G40060.3 (Glycine max), 3'ss of exon 4
---ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtt-----tggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
   ||   |  ||    |||||        | | || || ||| | | ||  | | | || |  |  |  |||  |||| ||||     |   ||| ||   |||||||||||||||||||||||| | ||||||||||||||||| || ||| | ||   ||  || || || || ||||| || |||| || |||||   ||||| 
gagtttcataactttgctatta-----ccttctagaaat-tcagagtatgcca-tgatcaatgag-ttaatgaaaattaatgttatacctctaatttgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCTGAAA

upper sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G00740.3 (Glycine max), 3'ss of exon 4
--------ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
        || |  | ||   |  ||    ||   |  |  |||  ||  ||   | | | |  | |   | |    | | ||||   |      ||   | |||||||||||||||||||||||| | ||||||||||||||||  || ||| | ||   ||  || || || || ||||| || |||| || |||||   | ||| 
gaattaaattatcctactattaccttctaaaa-attcagagtatgccatgatcaatgagtta--actaaaatt----aatgttatacctctaatctgtcat-ttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGCATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCAGAAA

upper sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G12980.2 (Glycine max), 3'ss of exon 4
--------ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
           || |  ||| ||||   || || || ||  ||| | | | |  | |  |    | |   || | |  ||   |    |   | ||  |   |||||||||||||| ||||||||||| |||||||| |||||||| || ||| | ||  |||  || ||  |||| |||||||| |||| || |||||   ||||||
tagctgacagtttgttttgccatat---gggat-atatgtttatgttagattaagcagttgtttagt--aacatttatgtgaaacctctaaatttt--tcatttgcagTTGAGGAATTTGGTTTGGTCAACATCAAAACATGATGTATATCTTGTTTCAAATTACTCCATTGTTCACTGGTCTTCATTAACTTCCAAGAGATCTGAAG

upper sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G02070.1 (Glycine max), 3'ss of exon 4
------ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
       |       ||   |  ||      ||| |   | | | | | |  | |  |    | |   || | |  ||   |    |   | ||  |   |||||||||||||| ||||||||||| |||||||| ||||| || || ||| | ||  |||  || ||  |||| |||||||| |||| ||  ||||   ||||| 
tgatagctgacactttgttttgctatatgg-gatatatgtttgttagattaagcagttgtttagt--aacatttatgtgaaacctctaatttttcat---ttgcagTTGAGGAATTTGGTTTGGTCAACATCAAAACATGACGTATATCTTGTTTCAAATTACTCCATTGTTCACTGGTCTTCATTAACTTCTAAGAGATCTGAAA

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|161705531|gb|FC057533.1|FC057533
EST:     AATTCTGGCGAAACACAAGATCTGTGAAATCGACCATCCTTCATTTCCAA                         TTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCT
genomic: AATTCTGGCGAAACACAAGATCTGTGAAATCGACCATCCTTCATTTCCAAgtatgctgat ... tgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCT
EST: gi|30138095|gb|CB923433.1|CB923433
EST:     AATTCTGGCGAAACACAAGATCTGTGAAATCGACCATCCTTCATTTCCAA                         TTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCT
genomic: AATTCTGGCGAAACACAAGATCTGTGAAATCGACCATCCTTCATTTCCAAgtatgctgat ... tgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
            ttctgac  putative branch site (score: 2)
                          tattattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtttggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - tcctgca
- - - - - - - - - - ggaatga
- - - - - - - - - - - - - - - - - - -tcaaaat
- - - - - - - - - - - - - - - - - - - - - - - -taaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgg