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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTTATAAAGTTTGCTCCTGCATATTTCAAGTACCTATCTGAATCAATCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctgagggcttcaaatgacaattagactagattgtcagtgcccacattaacctgacatttgctaagatctaccacccatattgaaatgctggta...

Basic information

species Vitis vinifera
transcript Vv09s0002g00380.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA16G01590.1 (Glycine max), 5'ss of exon 11
ATCATTTATAAAGTTTGCTCCTGCATATTTCAAGTACCTATCTGAATCAATCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatt--tcctgagggcttcaaatgacaattagactagattgtcagtgcccacattaacctgacatttgctaagatctaccacccatattgaaatgctggta---
 ||||| || || |||| ||||| ||| ||||||||||| |||||||| ||  |||| ||||||||||| ||| ||||||||||||| || || ||||||||| |  || |  | || | | ||     ||    |   || |  |  ||      ||  | | |  | ||||    |||     | | |||||  ||| |    
GTCATTCATTAAATTTGGTCCTGAATACTTCAAGTACCTTTCTGAATCCATAGGCACCGGAAGTCCAACTTGCCTGGCAAAGATTCTTGGCATATACCAGgtactggtcttctgagccttacattttctttttcttttgttttttggacct---caaatgtcatagcttctaaa--ttactggtgaaaatgaaaacctgttgagt

upper sequence: Vv09s0002g00380.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA07G05100.1 (Glycine max), 5'ss of exon 10
ATCATTTATAAAGTTTGCTCCTGCATATTTCAAGTACCTATCTGAATCAATCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtattt--cctgagggcttcaaatgacaattagactagattgtcagtgcccacat-taacctgacatttgctaagatctaccacccatattgaaatgctggta
 ||||| || || |||| ||||| ||| ||||||||||| |||||||| ||  |||| |||||||| || ||| ||||||||||||| || || ||||||||| ||  | |  | || | | ||     ||    |    | |  ||      |  | |  || |||    |   |  |||     | | |||||  |||   
GTCATTCATTAAATTTGGTCCTGAATACTTCAAGTACCTTTCTGAATCCATAGGCACTGGAAGTCCGACTTGCCTGGCAAAGATTCTTGGCATATACCAGgtacttgtcttctgagccttacattttttttttctttttcttttggtttttggacctcaaatgtcatagcttctaaattactggtgaaaatgaaagcctg---
















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|349814824|gb|FQ410047.1|FQ410047
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|351023163|gb|FQ432546.1|FQ432546
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|351037296|gb|FQ457129.1|FQ457129
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349813704|gb|FQ413938.1|FQ413938
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349813666|gb|FQ413900.1|FQ413900
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349811550|gb|FQ409546.1|FQ409546
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349823260|gb|FQ400239.1|FQ400239
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|30128919|gb|CB914258.1|CB914258
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349821544|gb|FQ408103.1|FQ408103
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGGAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349809534|gb|FQ414424.1|FQ414424
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|352791391|gb|FQ480970.1|FQ480970
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349814303|gb|FQ398743.1|FQ398743
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349807510|gb|FQ401503.1|FQ401503
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349813926|gb|FQ414160.1|FQ414160
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349811257|gb|FQ406245.1|FQ406245
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349816603|gb|FQ399592.1|FQ399592
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349814433|gb|FQ398873.1|FQ398873
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349815793|gb|FQ400949.1|FQ400949
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
EST: gi|349819795|gb|FQ404517.1|FQ404517
EST:     TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAG                         GTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG
genomic: TCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctg ... atgttggaagGTTACGTCCAAGCATCTGAAAGGAGGGAAGGAATCAAGGATGGATCTTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATTTATAAAGTTTGCTCCTGCATATTTCAAGTACCTATCTGAATCAATCAGCACGGGAAGTCCAACATGCTTGGCAAAGATTCTGGGGATTTACCAGgtatttcctgagggcttcaaatgacaattagactagattgtcagtgcccacattaacctgacatttgctaagatctaccacccatattgaaatgctggta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgaaa