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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttactcatgttaaagggttgttgattttgtctgcactacagttccacatatagtgcacattttcactttgtacagcagactgatgtataatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGC

Basic information

species Vitis vinifera
transcript Vv00s0250g00020.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G34370.1 (Glycine max), 3'ss of exon 7
ttttactcatgttaaagggttgttgattttgtc---tgcactaca---gttccacatatagtgcacattttcactttgtacagcagactgatgtataatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGC
   ||   |     | || |  |  ||| || |   | || ||     | |     | |  ||  | | ||||| || ||       || |  |   || | ||||||||||||||||||||||| |||||  ||  ||||||||||| || ||||||||||||||||| ||||||   ||||||||||| || |||||||| |||
---taactaaac--agggatcatatattctgccttttacattatgttggctttgtttgtcatgttcttcttcacattataggatgatctaacatg-gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGC

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G33190.1 (Glycine max), 3'ss of exon 7
ttttactcatgttaaagggttgttgattttgtctgcacta--cagttccacatatagtgcacatt-ttcactttgtacagcagactgatgtataatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGC
 | ||   |     |  | |  |  ||| || ||     |  | ||| |   | |    ||  || ||||| || || |     || |  |   || | ||||||||||||||||||||||| |||||  ||  ||||||| ||| || ||||||||||||||||| ||||||   ||||||||||| || |||||||| |||
gtgtaactaaac--agtgatcatatattctgccttttacattctgttgcctttgtttgtcatgttcttcacattatagaatgatctaacatg-gatgtagcagGGACTTTGATGCATTTGATCTACGGAGGCGGCTTCCAGTTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGC
















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|37188932|gb|CF608281.1|CF608281
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|30252735|gb|CB970286.1|CB970286
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|110731715|gb|EE106367.1|EE106367
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|110725728|gb|EE102561.1|EE102561
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|110390476|gb|EC955386.1|EC955386
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|27582920|gb|CB005615.1|CB005615
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|110719002|gb|EE096483.1|EE096483
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
EST: gi|71858350|gb|DT007405.1|DT007405
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGC
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGC
EST: gi|110723499|gb|EE100881.1|EE100881
EST:     GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAG                         GGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA
genomic: GAATATGCCAATACATTTGATGACATTCAACACTTGCGAGCTGAAATAAGgttagtcatg ... aatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacatatagtgcacattttcactttgtacagcagactgatgtataatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGC
                                  gactgat  putative branch site (score: 3)
                                       atgtataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttactcatgttaaagggttgttgattttgtctgcactacagttccacatatagtgcacattttcactttgtacagcagactgatgtataatctggcagGGACTTTGATGCATTTGATTTACGGTTGCAACTTCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - -ctcatgt
- - - - - - - - gggttgt
- - - - - - - - - - - - - - -tgtctgc
- - - - - - - - - - - - - - - - - - - - - - -ccacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt