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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttatttaatagcttagatgattgatgagattagaacatggtcttagaggaagaactttgatatggtgttctgaacttcatacattgcatcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGTGACCTGTTTCAAAGTTTTGGATTTGATACACAGCCAGTTCTCATTGGCC

Basic information

species Vitis vinifera
transcript Vv15s0046g02040.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 10
-------tttttatttaatagc--ttagatgattgatgagattag--aacatggtcttagaggaagaactttgatatggtgttctgaacttcatacattgcatcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGTGACCTGTTTCAAAGTTTTGGATTTGATACACAGCCAGTTCTCATTGGCC
        ||  ||| |||     ||| ||| || |||  |  ||  |      | || ||  | ||  ||   | |  || | |||      || ||||      || ||||||||||| |  | |||||||||||||||||||| ||| | || || | ||| |||| || ||| ||||| |||||||| |||||||| |||||||| |
cctcatagttacattcaattataattaaatgtttaatggaaaaaggcattgcaatatttgactatgagattatttgtaatgctttga------tatattgt-----tgtagATTCTTACACTTCTACAATTTGGAGGATATACACTAGTGCGAAATTCAGCTGATCTGTATCGAAGCTTTGGGTTTGATACGCAGCCAGTCCTCATTGGGC

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 9
tttttatttaatagcttagatgattgatgagattagaacatggtcttagaggaagaactttga-tatggtgttctgaacttcatacattgcatcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGTGACCTGTTTCAAAGTTTTGGATTTGATACACAGCCAGTTCTCATTGGCC-
  | |  |   ||  ||  || ||   | |   |  ||             | |  | ||||| |  | |  | || |   | |  ||   ||   || ||||||||||| |  | |||||||||||||||||||| ||| | || ||   ||| |||| || ||| ||||| |||||||| |||||||| |||||||| | 
-ctctcatagttacattcaattataattaaatgtttaatggaaaaggcattgcaatattttgactgagattatttgtaacactttgat-atattgttgtagaTTCTTACACTTCTACAATTTGGAGGATATACACTGGTGCGAAATTCAACTGATCTGTATCGAAGCTTTGGGTTTGATACCCAGCCAGTCCTCATTGGGCT

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 10
----tttttatttaatagcttagatgattgatgagattagaacatggtcttagaggaagaactttgatatggtgttctgaacttcatacattgcatcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGTGACCTGTTTCAAAGTTTTGGATTTGATACACAGCCAGTTCTCATTGGCC
       | |    | || | | |   ||  | | ||    |  |    | |||         ||   |||    |||   ||  ||   |||| |    |||||| ||| | ||||| |||||||||||||| || ||||| || |||||   ||| || ||    ||||| ||||||||||||||||| |||||||||||  
gtgaggctcaaccgacagttcaaaaacttactcacatctacatttcacttaagaaatcatgtctt---atgaccctct---ctcaatgttttgctt----gcagATCCTTGCCTTCTTACAATTTGGAGGATACACTCTTGTCAGAAACTCCACTGATCTCTTCAGGAGTTTCGGATTTGATACACAGCCTGTTCTCATTGGTT

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|349814570|gb|FQ399210.1|FQ399210
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|30304044|gb|CB980838.1|CB980838
EST:     TGGGGCATTGGAAACTTAATCGTACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351052220|gb|FQ452374.1|FQ452374
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351043081|gb|FQ451254.1|FQ451254
EST:     TGGGGCATTGGAAGCTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|110387119|gb|EC951763.1|EC951763
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351012828|gb|FQ430391.1|FQ430391
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351045038|gb|FQ449292.1|FQ449292
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGTAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|30304107|gb|CB980901.1|CB980901
EST:     TGGGGCATTGGAAACTTAATCGTACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351040629|gb|FQ438173.1|FQ438173
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351033796|gb|FQ447834.1|FQ447834
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|349820667|gb|FQ408496.1|FQ408496
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351044625|gb|FQ443156.1|FQ443156
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351043828|gb|FQ452622.1|FQ452622
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351029807|gb|FQ427647.1|FQ427647
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
EST: gi|351052441|gb|FQ452474.1|FQ452474
EST:     TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAG                         ATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT
genomic: TGGGGCATTGGAAACTTAATCATACAATGTACTCTTTCATTGCTGTGCAGgtatgctgcc ... atcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaggaagaactttgatatggtgttctgaacttcatacattgcatcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGTGACCTGTTTCAAAGTTTTGGATTTGATACACAGCCAGTTCTCATTGGCC
            ctttgat  putative branch site (score: 5)
             tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttatttaatagcttagatgattgatgagattagaacatggtcttagaggaagaactttgatatggtgttctgaacttcatacattgcatcaatgcagATTCTTACATTCTTGCAATTTGGAGGATATACACTTGTGAGGAACTCGGGTGACCTGTTTCAAAGTTTTGGATTTGATACACAGCCAGTTCTCATTGGCC

- - - - - - - - - - - - - - - - - - - catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - ggaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacat