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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccttctcttttaaggttgtaattctaagaattccagttctggataaaaagaacagatatttccagaagagcttttgagtaatatctcaaccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTGAGCCGATCTTTTGAATTTCAG

Basic information

species Vitis vinifera
transcript Vv15s0046g02040.t01
intron # 11
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 11
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 10
gccttctcttttaaggttgtaattctaaga-attccagttctggataaaaagaacagatatttccagaagagcttttgag----taatatctcaacct-tttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTGAGCCGATCTTTTGAATTTCAG-
        |   ||| |||    || | |  |||    || |  |     |    |||| ||  |   | |||  || |     |   | ||  |  | ||||||||||||||| || || || |||||  | || ||||||||||| || ||||| |||||||| |||||||||||| 
-------atccaaagtttgagcctccatgccattattcttttatagttccatggaagattttatctacaaagcacttaaaatcctttcacctggatttatttgcagcATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTTGTCAGCCGATCATTTGAATTTCAGG

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 11
gccttctcttttaaggttgtaattctaagaattccagttctggataaaaagaacagat-atttccagaagagct--tttgagtaatatctcaacct-tttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTGAGCCGATCTTTTGAATTTCAG
     |   |||   |     || | |  | |     |  | | |     ||| |  | |||| || |  |  |  | |   |   | ||  |  | ||||||||||||||| || || || |||||  | || ||||||||||| || || || |||||||| ||||||||||||
----ccaaattttgagcctccatgccattattctttttcatagttccttggaagattttatttacaaagcacttaatatccttttcacctggatttatttgcagCATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTAGTCAGCCGATCATTTGAATTTCAG
















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:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|30304044|gb|CB980838.1|CB980838
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|351052220|gb|FQ452374.1|FQ452374
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|110373389|gb|EC937620.1|EC937620
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|110391978|gb|EC957064.1|EC957064
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|351043081|gb|FQ451254.1|FQ451254
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|110387119|gb|EC951763.1|EC951763
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|351012828|gb|FQ430391.1|FQ430391
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCT
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCT
EST: gi|351045038|gb|FQ449292.1|FQ449292
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAAGCTTTGGTCTTAATCTT
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAA-GCTTTGGTCTTAATCTT
EST: gi|30304107|gb|CB980901.1|CB980901
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTT
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTT
EST: gi|351040629|gb|FQ438173.1|FQ438173
EST:     GTTATGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTT
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTT
EST: gi|351033796|gb|FQ447834.1|FQ447834
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|349820667|gb|FQ408496.1|FQ408496
EST:     GTTTTGGATTTGATGCACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|351044625|gb|FQ443156.1|FQ443156
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|351029807|gb|FQ427647.1|FQ427647
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
EST: gi|351052441|gb|FQ452474.1|FQ452474
EST:     GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAG                         CATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG
genomic: GTTTTGGATTTGATACACAGCCAGTTCTCATTGGCCTCATCATATTTCAGgtattgatat ... ccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaagaacagatatttccagaagagcttttgagtaatatctcaaccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTGAGCCGATCTTTTGAATTTCAG
                                             ccttttgc  CT-rich tract
         agatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccttctcttttaaggttgtaattctaagaattccagttctggataaaaagaacagatatttccagaagagcttttgagtaatatctcaaccttttgcagCATACTGTGATACCTCTCCAGCACCTTGTAAGCTTTGGTCTTAATCTTGTGAGCCGATCTTTTGAATTTCAG

-ccttctc
- - - - - - - - - - - - - - - - - - gttctgg
- - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - gaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaagag