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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttcttaacaccctgttttttatttgaatgtttccgtagttgtattaaaatcaaatcaaagccatcaatgaacaaaagatacttccatttggcat...

Basic information

species Vitis vinifera
transcript Vv09s0002g00390.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os12g31380.1 (Oryza sativa), 5'ss of exon 3
GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttcttaa--caccctgttttttatttgaatgtttccgtagttgtattaaaatcaaatcaaagccatcaatgaacaaaagatacttccatttggcat--
||||||||||| ||| |||| |||||||  || |||||||| ||||||||||| |||  ||| |||   ||    ||||||||  | ||  | |||||||||   ||  | ||    |  |      |   |  |  ||| |  | || ||| |||     | |||   ||| | |  ||| |     |||     |||     
GATGGTTGTACTATTCTGGTACATGGTTATTCCAGAGTTGTTTTGGAAGTTCTAAAGCTAGCTGCATCAAACCGCAAACTCTTCAGGGTACTTTGCACAGgtaaattgatcaagttgcatttgaaactgcatctacattttca-aattttatcaaagatgcaacaa---cattattctacacagacagcttggtgatggtgaac

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA03G42430.1 (Glycine max), 5'ss of exon 3
GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttcttaacaccctgttttttatt-tgaatgtttccgtagttgtattaaaatcaaatcaaagccatcaatgaacaaaagatacttccatttggcat---
||||| || || |||||||| |||||||| || ||||||||||| ||||| || ||    || ||||| ||||| ||||| ||||| || |||||||||||||| |  | |    |   || | ||| | |   | | |     ||  |   |||| |||| | |   ||| | | | |  || |   |    ||         
GATGGCTGCACAATTTTGGTTCATGGTTTTTCCAGAGTTGTCTTTGAAGTCCTAAAACTTGCTGCACAAAATAACAAACTATTTCGGGTCTTCTGCACAGgtttttgccct----cttagtctcttactctcgttatatagactgtcttggcaaaagcaaaactagttcataacttagctgaaaactttaaagttaattgaagg

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G05070.1 (Glycine max), 5'ss of exon 3
GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttcttaacaccctgttttt-tatttgaatgtttccgtagttgt-attaaaatcaaatcaaagc-----catcaatgaacaaaagatacttccatttggcat
|| || || || ||| | || || || |||||  |||| ||  |  |  |||| ||    || || |||||||| || |||||||| || |||||||||||||| ||||||     | | | | | | | |   ||| || || ||| | | |   | ||| |    |      | | |||   |||   ||||  | | |      
GACGGCTGCACGATTCTCGTTCACGGATTCTCCCGAGTCGTGCTTCAGATTCTCAAACTCGCCGCGCAGAATAACAAGCTCTTTCGCGTCTTCTGCACAGgtttttttctttttttcttctctctatctctctttgtgtctgttgttttcaatgttagcaatttgtggtttgaactttaatttgcaagt-ataccacgaat------

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G72340.1 (Arabidopsis thaliana), 5'ss of exon 3
GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttcttt----------ctta----acaccctgttttttatttg---aatgtttccgtagttgtattaaaa-----tcaaatcaaagccatcaatgaacaaaagatacttccatttggcat-------------------------------------------------
|||||||||||||| ||||| |||||  |||||||||||||  ||||| | || ||||| || ||||| || || || |||||||||||| ||||||||||||   ||          ||||      | | ||  || |||  |   ||||||||  | |||    | | |     |     || || | | |    | |||   |   ||  | ||   |                                                 
GATGGTTGTACCATATTGGTTCATGGACTCTCTAGAGTTGTTCTGGAAATACTTAAGACTGCTGCACAAAACAACAAGCTCTTTCGAGTTCTCTGCACAGgttcgcttaaacaacaagcttagattggaacttgagttgtatccgcttaatgtttct-tggtttctctgagacatttttgttgcatagtcttgaccttataaaccctgtctctttatgattttgttgtattagtagcctctcgctaactttttttggtgaaaaaatgatag

upper sequence: Vv09s0002g00390.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G53880.1 (Arabidopsis thaliana), 5'ss of exon 5
GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttcttaacaccctgttttttatttga-atgtttccgtagttgtattaaaatcaaatcaaagccatcaatgaacaaaagatacttccatttggcat------------
||||| ||||| ||| |||| ||||||||||| |||||||| || ||| | || |||||| |||| || || ||||||||||||||||| || |||||||||   |||||||| ||   |   |  ||| || |||    | |     |||   | ||  ||       |   |  | || |      || |||  |                
GATGGGTGTACTATTCTGGTCCATGGTTTCTCCAGAGTTGTGTTTGAAATACTAAAGACATCAGCGCAAAACAAGAAACTCTTTCGAGTGTTGTGCACAGgtacttttcttaagacttagagatcaattggatatgacatcttccagttatctcattctgattttcctaactgacaatcacatttccgttgcatccgtggaaacaaaatacag

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|110399161|gb|EC965654.1|EC965654
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCGGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|110375926|gb|EC940956.1|EC940956
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCGGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|351044484|gb|FQ443015.1|FQ443015
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCCAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|349807839|gb|FQ402230.1|FQ402230
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|349817476|gb|FQ407266.1|FQ407266
EST:     TCTGAAGACAGCAGCGCAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|351012185|gb|FQ426907.1|FQ426907
EST:     TCTGAAGACAGCAGCGCAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|349814725|gb|FQ409948.1|FQ409948
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|110372726|gb|EC936913.1|EC936913
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCGGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|351024997|gb|FQ433414.1|FQ433414
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCCTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|349822671|gb|FQ412935.1|FQ412935
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|351053555|gb|FQ459302.1|FQ459302
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGACAA-G
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGG-CAAAG
EST: gi|351049282|gb|FQ429025.1|FQ429025
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCCATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|110406357|gb|EC971927.1|EC971927
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|349821346|gb|FQ404478.1|FQ404478
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|351048077|gb|FQ441249.1|FQ441249
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|351031133|gb|FQ444960.1|FQ444960
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCCAATGAA-TGGCAAAG
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCC-AATGAAATGGCAAAG
EST: gi|351056004|gb|FQ453465.1|FQ453465
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|352790509|gb|FQ478149.1|FQ478149
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTCCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|349822083|gb|FQ408412.1|FQ408412
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCAGACAGGACAGGACTACGACTATCCCATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
EST: gi|110392389|gb|EC957773.1|EC957773
EST:     TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAG                         AGGGAAGGCCGGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC
genomic: TCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttct ... taaaatgcagAGGGAAGGCCAGACAGGACAGGACTACGACTATCCAATGAAATGGCAAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGTTGTACCATTTTGGTGCATGGTTTCTCTAGAGTTGTCTTGGAAGTTCTGAAGACAGCAGCACAGAATAAGAAACTCTTTCGAGTTTTCTGCACAGgtttctttcttaacaccctgttttttatttgaatgtttccgtagttgtattaaaatcaaatcaaagccatcaatgaacaaaagatacttccatttggcat

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa