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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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcattcctttatgactgagtccctgattcatgttgctttatgtgtgtggcagttttttgtttttgctattgttttaatttttgtggtgtcaaattatgaaggcctgtaatgaatttcttggttgtaatttctcaagtttgattattaaattgtgttatctgtttggcagGTTGACGAAGAACTAGACGAATTAATTTCACGGATAAAGCTGCAAGAAGGTAATACAGAGTTCTGGAAGCGTCGCTTCCTTGGAGAGGACTTGACTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA