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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcattcctttatgactgagtccctgattcatgttgctttatgtgtgtggcagttttttgtttttgctattgttttaatttttgtggtgtcaaattatgaaggcctgtaatgaatttcttggttgtaatttctcaagtttgattattaaattgtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG

Basic information

species Vitis vinifera
transcript Vv04s0043g00700.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0043g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os10g32540.1 (Oryza sativa), 3'ss of exon 9
gttaatcattcctttatgactgagtccctgattcatgttgctttatgtgtgtggcagttttttgtttttgctattgttttaatttttgtggtgtcaaattatgaaggcctgtaatgaatttcttggttgtaatttctcaagtttgattattaaattgtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG
| || | || || || || | | | || | ||| | ||| | | || |||| | | | | | ||||| | | ||| ||||||| ||||| |||| ||||| |||||||| || ||||| |||| || ||||||||||| |||||||| || ||||| ||||| || | |
-------------------------------------------------------------gtaagttgacaatatttactgcattagtcctatttggtggtgttatcatgtgagaaatgt--tacctgctatttttt--gctgaagttttaaagtacaacacta--ttgatagGTTGATGAAGAGTTAGATGAATTGATTTCACGAATCAAGCTAGAAGATGGGAATACAGAGTTTTGGAAGCGGCGTTTCCTGGGAGAAACTCGGAATTATC

upper sequence: Vv04s0043g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G31180.1 (Glycine max), 3'ss of exon 9
gttaatcattcctttatgactgagtccctgattcatgttgctttatgtgtgtggcagttttttgtttttgctattgttttaatttttgtggtgtcaaattatgaaggcctgtaatgaatttcttggttgtaatttctcaagtttgattattaaatt---gtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG
||| ||| || | || ||| | | || ||| | | ||| | || | | | | | || |||| | ||| || | | ||||| |||||||| || || | |||||||||||| ||||||||| | ||||| ||||||||||||||||| |||||||| | ||||| | ||| | || ||
------------------------------------------------------------------------gttgattt--cttcatttgtttca---tctaaatacctttttcttttctctccatctggatctttaatatataatgcctaaacttaaatgtgattcatattccagGTGGACGAAGAGCTGGATGCATTAATTTCACGTATAAAGCTGGAGGAAGGAAATACAGAGTTCTGGAAACGTCGCTTTTTAGGAGAAGGCTTAAATGGTG

upper sequence: Vv04s0043g00700.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G36340.1 (Glycine max), 3'ss of exon 9
gttaatcattcctttatgactgagtccctgattcatgttgctttatgtgtgtggcagttttttgtttttgctattgttttaatttttgtggtgtcaaattatgaaggcctgtaatgaatttcttggttgtaatttctcaagtttgattattaaatt---gtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG
|| ||| || ||| ||| | || ||| | | ||| | | || | | | | | || |||||| ||| || | | ||||| || ||||| || || | ||||||||||| ||||||||| | ||||| ||||||||||||||||| |||||||| | ||||| | ||| | || ||
-----------------------------------------------------------------------------gttgattcttcatttgttttatt-taaatacctttttcttttctctccatcttgatctttaatatataatgcctaaatttaaatgtgattcatattccagGTGGATGAAGAGCTGGATGCATTAATTTCACATATAAAGCTGGAGGAAGGAAATACAGAGTTCTGGAAACGTCGCTTTTTAGGAGAAGGCTTAAATGGTG

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|71876898|gb|DT025953.1|DT025953
EST:     CACGTGGTCGTCCCCTTTGGGTTCCTCCTGTGGAGGAGGAGGAAGAAGAG                         GTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGT
genomic: CACGTGGTCGTCCCCTTTGGGTTCCTCCTGTGGAGGAGGAGGAAGAAGAGgttaatcatt ... tgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGT
EST: gi|71871885|gb|DT020940.1|DT020940
EST:     CACGTGGTCGTCCCCTTTGGGTTCCTCCTGTGGAGGAGGAGGAAGAAGAG                         GTTGACGAAGAACTAGACGAATTAATTTCNACGGATAA-GCTGCAAGAAGG
genomic: CACGTGGTCGTCCCCTTTGGGTTCCTCCTGTGGAGGAGGAGGAAGAAGAGgttaatcatt ... tgtttggcagGTTGACGAAGAACTAGACGAATTAATTTC-ACGGATAAAGCTGCAAGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttggttgtaatttctcaagtttgattattaaattgtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG
                     gtttgat  putative branch site (score: 5)
 tctgttt  putative PPT
 taatttctcaagtttg  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcattcctttatgactgagtccctgattcatgttgctttatgtgtgtggcagttttttgtttttgctattgttttaatttttgtggtgtcaaattatgaaggcctgtaatgaatttcttggttgtaatttctcaagtttgattattaaattgtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA