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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaagaaattatggcttgaattcttttttgaattcattattataaggatggagtttctataagtttactttcgtcctccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC

Basic information

species Vitis vinifera
transcript Vv02s0033g00260.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g16240.1 (Oryza sativa), 3'ss of exon 2
gtaatcaagaaattatggcttgaattcttttttgaattcattattataaggatggagtttctataagt--ttactttcgtcctccattg---tgtagGTCTT----------------GACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC
             | |||||    | ||||||| |  |||||| |  | || |  | |||| |  | |  |||   |       |||||   || |  | ||                || | |||    ||||| ||||||  ||||||||| ||||||| ||| |||||||| ||||||||||| || || || ||  | ||||  |||||
-------------tttggctatgttccttttttaatatcattactcaaggggttaaatttcaaacaatgattaacctaacttatcattgatatgcaattttttatgcaagcagATACAGATTTTGCTCATCAAGTGGGAGTAACACATTTCTACCACATTTTCTACGAAGGTTGCTTAACAAACTTCGACATTGGTGACAATGGAGCCGAAGC

upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 2
-----------gtaatcaagaaattatggct--tgaattcttttttgaattcattattataaggatggagtttctataagtttactttcgtcctccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC
            |  |  | | |  ||  ||  ||   |    ||| ||   ||||||     ||   |  |   ||   | | |  |  |  |       | || | |  | | |||    ||||| ||| ||  ||||||||| ||||||| ||| || ||||| |||||||||||||| || || ||  | ||||  |||||
agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattatt-----gacctaactatcattgATATGCAATTTTTTTAATGCAAGCAGATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC

upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 3
-----------gtaatcaagaaattatggcttgaattcttttttgaattcattattataaggatggagtttctataagtttactttcgtcc-tccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC
             |  |   | |  | |   |||||| |||    ||||||||  ||| |  |   |      | ||  | |||||  |   |      |  |||| | |||||||| |  ||||| || || || ||||||||||| |||| ||||||||||||||| ||||||||||||||||| ||||  |||||||||||
gtaaaaaaaatacaccccgaagagaaagaactgaattatttgactaattcattcatatcatcaacaaaa----aaaaaatgactttgattaatgtgagttacagGTTTGGACTATGCAGCTCAAGTGGGGGTGGGGCATTTCTATCATATTTTCTATGAAGGTTGTTTGACAAACTTTGAAATAGGAGAAGGTGGAGAAGAAGC

upper sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G32100.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------gtaatcaagaaattatggct--tgaattcttttttgaattcattattataaggatggagtttcta-taagtttactttcgtcctccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC
                                    |  ||   ||  |||   |  ||        |||   |  ||| | | ||  || |    || | |   |||  |||| |   |   | |||||   | ||   | |   |||||  ||  ||||||||||||||||||||| ||||||||| ||| | ||  |    ||| | || ||||| | |||||   |
gtaagtccaagcaatagtgtaacgtaatctactttatgttcggcaacatatccttaatgggccaggctttaggtctatt-tgaaaaatatagcccatcaactttatttgatttcttttacatgtatgtagAAATGGAGATTCCACACCAAGCAGGGATAGGACATTTCTATCACATTTTCTATGAAGGATGTCTCACTGATCACGAAGTCGGAGAAGACGAAGAAGCTTC

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|33407732|gb|CF213359.1|CF213359
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTTTGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|33408350|gb|CF213977.1|CF213977
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|33409205|gb|CF214832.1|CF214832
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTTTGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|33407646|gb|CF213273.1|CF213273
EST:     GCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTTTGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: GCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|33408357|gb|CF213984.1|CF213984
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGT-GATACATTTCTATCACATTTAC
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGG-ACATTTCTATCACATTTAC
EST: gi|33409691|gb|CF215318.1|CF215318
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGTAGG
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGG
EST: gi|33408614|gb|CF214241.1|CF214241
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|33410196|gb|CF215823.1|CF215823
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|351016398|gb|FQ423825.1|FQ423825
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|110414926|gb|EC980789.1|EC980789
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
EST: gi|33410413|gb|CF216040.1|CF216040
EST:     ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAG                         GTCTTGACTTTGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT
genomic: ACTAGACAAGTCTAGCATCTCTGCAGAAGAATTCCTCGTCTCCATGAAAGgtaatcaaga ... cattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattattataaggatggagtttctataagtttactttcgtcctccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC
                              tttactttcgtcctcc  CT-rich tract
                    tttctataagttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcaagaaattatggcttgaattcttttttgaattcattattataaggatggagtttctataagtttactttcgtcctccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC