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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggcttttatatagttaatttttttttcttgccattatt...

Basic information

species Vitis vinifera
transcript Vv15s0046g02040.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 9
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggcttttatatagttaatttttttttcttgccattatt
|| || |||||||| || || || |||||||| || || ||||||||||| ||||||||||||||    |     |   || ||| |   ||| |||  |  |||    || |||||   | | |  ||    |  |     || |   ||   |        
GCTTACATGTATGGGTTTTTCAAGAACAAGCGCATTGTTCTCTATGACACGTTGATTCAGCAGgtt---atatgctaagttgtttag---tttcattataattttg---aattacatg--catgaaactcacctggatccttttgtcggtttcag--------

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM5G813909_T01 (Zea mays), 5'ss of exon 9
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgt--ggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggcttttatatagttaatttttttt-tcttgccattatt--
||||| |||||||| || || || |||||||| ||||| |||||||||||||||||||||||||| |   ||  || | | || | |   || |||        ||| | | |  | |||||    | || |  | | | || |  | |||  | |||    | |   
GCCTACATGTATGGTTTTTTCAAGAACAAGCGCATAGTACTCTATGACACATTGATTCAGCAGgtatcttgaaacaatattttttctaacaacttttaagttattttgtttcataaaatattggc-atgcatgcacagaattgacctgtttcattttgttgatttcag

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G702159_T01 (Zea mays), 5'ss of exon 9
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggc-ttttatatagttaatttttttttcttgccattatt
|| || ||||||||||| ||||| || || || ||||| ||||||||||||||||||||||||||          |  ||  ||   | ||||| ||| |      |    || || |   || |    |||| | | ||| ||||                  
GCTTACATGTATGGATTTTTTAAGAATAAACGCATAGTACTCTATGACACATTGATTCAGCAGgt----------tcaatccttcaaacattttgtttcataaaaattggcatgcacagaattgacctgttttcttttgttgatttcag---------------

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA09G39150.1 (Glycine max), 5'ss of exon 9
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggctttta---tatagttaatttttttttcttgccattatt
|||||||||||||||||||| || |||||| |||| ||||| ||||||||||| ||||| |||||  |||   | |      | | || ||||  |||    |||   |  ||| | | |  ||  | |||     | |||   |  ||| |||||    | |   
GCCTATATGTATGGATTCTTCAAGAACAAGAGGATTGTCCTTTATGACACATTAATTCAACAGgttaggaattactactaactgtagagatttattttgtcttttaggttgatatacagttcttgtgttttagccttttagaagagctttatttctgtaaaat---

upper sequence: Vv15s0046g02040.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA18G47190.1 (Glycine max), 5'ss of exon 8
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttt---tctaaatacatattct-ttaggcttttatatagttaatttttttttcttgccattatt
 ||||||||||||||||||| || |||||| |||| || || ||||||||||| ||||| |||||   ||   | |  || | |    || |||||||   ||||    |    |||||| |  | ||      ||||  |     ||| ||| | |     | |  
-CCTATATGTATGGATTCTTCAAGAACAAGAGGATTGTGCTTTATGACACATTAATTCAACAGGttaagaattacta-ataactgtagaaatttattttgtctttcaggttgttatacatctcgtgttttaaccttatggaagagctttatttctataaaattca--

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:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|30304044|gb|CB980838.1|CB980838
EST:     GATTCTTTAACAACAAGCGGATAGTCCTGTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351052220|gb|FQ452374.1|FQ452374
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351043081|gb|FQ451254.1|FQ451254
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|110387119|gb|EC951763.1|EC951763
EST:     ATAGTCCTGTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: ATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351012828|gb|FQ430391.1|FQ430391
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCGGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351045038|gb|FQ449292.1|FQ449292
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|30304107|gb|CB980901.1|CB980901
EST:     GATTCTTTAACAACAAGCGGATAGTCCTGTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351040629|gb|FQ438173.1|FQ438173
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351033796|gb|FQ447834.1|FQ447834
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|349820667|gb|FQ408496.1|FQ408496
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351044625|gb|FQ443156.1|FQ443156
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351043828|gb|FQ452622.1|FQ452622
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
EST: gi|351029807|gb|FQ427647.1|FQ427647
EST:     GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAG                         TGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT
genomic: GATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggc ... tgttttgcagTGCAAAAAAGAGGAAGAAGTTGTTGCTGTTATAGCCCATGAACTGGGGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTATATGTATGGATTCTTTAACAACAAGCGGATAGTCCTCTATGACACATTGATTCAGCAGgtgtggaggcattttattatttggaaattttatttaagctttttctaaatacatattctttaggcttttatatagttaatttttttttcttgccattatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataca