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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgggttgtctgttcttctattttgacatatcctaaaggatgagagtctcttatacattatgcttttctggttattttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA

Basic information

species Vitis vinifera
transcript Vv09s0002g02500.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 9
tgttgggttgtctgttcttctattttgacatatcctaaaggatgagagtctcttatacattatgcttttctggt--tattttcttttgttggttt-tgttt--agGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA
       | ||    | |  |   || | | |  |||   | | | |  | |    ||| |   |   | || |  |||||  |  |||||| || | |||  ||| | ||||| | |||||||||||||||||| | |||||  ||||||||||||||  | || || || ||||| || || || |||||  | |||||||||
-----actagttacctgtattgaattaaaaaaaactatttgttcataagcacgatgacaatgctccagtgtgcttctatttattaatgttggcttctatttgcagGGTCCATTGTGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGA

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 9
tgttgggttgtctgttcttctattttgacatatcctaaagg----atgagagtctcttatacattatgcttttctggttattttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA
               ||  |  ||||||  | |  ||||      ||    | |  | | |   ||| || ||     || |   |||  |      |  ||||||| |||||  |||| |||  |||||| |||||||| || || || ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| 
----aaaagagacaatccacacttttgaagtttattaaaatgctcattgatgcccatgaaattgtatcctgtttaatgtagtcattttgataacaacttgttagGATTCATTGTCAAGAGAGTAATGAAGAAAGCTCAGAAACAGAGTCTGTTTATTCACTTAAATGCCACATATCACAGGAGGTGAACCATTTGCACGAAGGG

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 9
tgttgggttgtctgttcttctattttgacatatcctaaagg----atgagagtctcttatacattatgcttttctggttattttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA
         |    | |     ||||||  | |  ||||      |     |||  | | |   ||| |  ||     || |   |||  |      |  ||||||| |||||  |||| |||   ||||| ||||||||  | || || |||||||||||||||||||||||||| || ||||||||||||||||||||||| 
----aaagagagaatccacactttttgaagtttattaaaatgcttactgatgtccataaaattgtatcccgtttaatgtagtcattttgataataacttgttagGATTCATTGTCAAGAGAGTAAGGAAGAAAGCTCAGAAGCAGAGTCTGTTTATTCACTTAAATGCCACATATCGCAGGAGGTGAACCATTTGCATGAAGGG

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G21280.1 (Arabidopsis thaliana), 3'ss of exon 8
tgttgggttgtctgttcttctattttgacatatcctaaaggatgagagtctcttat-acattatgcttttctggttat-tttcttttgttggttttgttt-----agGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA
      ||            |   |  | ||  |||   | |||  | | | || | | ||  | | ||| || || | | |||    |   |||   ||     ||| |||||||| |||||||| | ||||| ||||||||||| ||||| || | ||| || ||||| ||||||||||| ||||||||||| ||||||||||||
------gtcacaacacaaatttcatacaaatgccctcttgtatgctattttttttttagatctttcatttttgattttgtgtctccaatccatttctattgctgaagGTTGCATTGCCAAGAAAGTAGCGAAGAAAGCTCAGAGACAGAATCTGTCTTTTCTCTGAAATGTCACATATCACATGAGGTGAACCACTTGCATGAAGGA

upper sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 8
tgttgggttgtctgttcttctattttgacatatcctaaaggatgagagtctcttatacattatgcttttctggtt--attttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA
 ||| |    | ||    |  |       | ||   ||    |||| |    || | ||   |||||   |  ||  |||    || |||  | |  | |||| |||||||  |||||||||| ||||| ||||||||||| ||||| || ||||| || ||||| || |||||||| || |||||||| ||||||||||||
-gtttgtccatgtgaaaattgacaactgaagatgtaaatacttgagtggtgttttt-caccttgcttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA

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|110422111|gb|EC988423.1|EC988423
EST:     AACTTTTTGGTGTTGAACTTGTTAGCAG                         GATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
genomic: AACTTTTTGGTGTTGAACTTGTTAGCAGgtatatattt ... ttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
EST: gi|110699590|gb|EE076722.1|EE076722
EST:     GAAAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAGCTTGTTAGCAG                         GATGCATTGCGAAGAAAGTGTTGAAGAGAGCTCAAAGACTGGAATCAGTTT
genomic: GAAAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAGgtatatattt ... ttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTG-AATCAGTTT
EST: gi|33405442|gb|CF211069.1|CF211069
EST:     TCTCGATACTGTGAAGGAAATTTGATGGTGTTGAACTTGTTAGCAG                         GATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
genomic: TCTCGATACTGTGAAGGAACTTT-TTGGTGTTGAACTTGTTAGCAGgtatatattt ... ttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
EST: gi|71873937|gb|DT022992.1|DT022992
EST:     AAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAG                         GATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
genomic: AAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAGgtatatattt ... ttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
EST: gi|71864100|gb|DT013155.1|DT013155
EST:     GAAAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAG                         GATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
genomic: GAAAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAGgtatatattt ... ttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA
EST: gi|33404796|gb|CF210423.1|CF210423
EST:     GAAAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAG                         GATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGGGACTGAATCAGTTTA
genomic: GAAAATCTCGATACTGTGAAGGAACTTTTTGGTGTTGAACTTGTTAGCAGgtatatattt ... ttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtctcttatacattatgcttttctggttattttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA
                                             ttttgttt  CT-rich tract
                            ttattttcttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgggttgtctgttcttctattttgacatatcctaaaggatgagagtctcttatacattatgcttttctggttattttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA

- - gggttgt
- - - - - - - - - - - - - - catatcc
- - - - - - - - - - - - - - - - - -taaagga