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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctcctctccacaccccccaccacatttctatacatttatcaaaccctaaaggtattttttttgaaattttgggcag

Basic information

species Vitis vinifera
transcript Vv01s0244g00010.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0244g00010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G882527_T04 (Zea mays), 5'ss of exon 4
ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctcctctccacaccccccaccacatttctatacatttatcaaaccctaaaggtattttttttgaaattttgggcag----------------------------------
 | | ||| ||| | ||  | ||||||||||| |||||||||||  ||||||||||||| ||||| |||||||||          | | |     |||        ||    ||   |   |||||  | |     ||  |  |     ||                                   
GTTACTGGAAAGGCCCTGATTCTGGATGAGATTATCAACTATGTGCAGTCCCTGCAGAACCAAGTTGAGgtaaaaaaagaaaaaaaaagcaggagccatgaagaattaa---tactcagtgctaaaaatgtggcacttctagctgacaacaatttgcaaatcatatactcctgcctgttttttcag

upper sequence: Vv01s0244g00010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G882527_T01 (Zea mays), 5'ss of exon 1
-------------------------------ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctcctctccacaccccccaccacatttctatacatttatcaaaccctaaaggtattttttttgaaattttgggcag----------------------------------
                                | | ||| ||| | ||  | ||||||||||| |||||||||||  ||||||||||||| ||||| |||||||||          | | |     |||        ||    ||   |   |||||  | |     ||  |  |     ||                                   
AGAAGGAACAAATGTGCTTTTTTTTGGACAGGTTACTGGAAAGGCCCTGATTCTGGATGAGATTATCAACTATGTGCAGTCCCTGCAGAACCAAGTTGAGgtaaaaaaagaaaaaaaaagcaggagccatgaagaattaa---tactcagtgctaaaaatgtggcacttctagctgacaacaatttgcaaatcatatactcctgcctgttttttcag
















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|110697604|gb|EE074737.1|EE074737
EST:     TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|110714473|gb|EE091418.1|EE091418
EST:     TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|32245670|gb|CD711489.1|CD711489
EST:     TACTGGATGAGATAATCAATTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|34416539|gb|CF415293.1|CF415293
EST:     TACTGGATGAGATAATCAATTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|110424499|gb|EC990862.1|EC990862
EST:     TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|30135269|gb|CB920607.1|CB920607
EST:     TACTGGATGAGATAATCAATTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|110695430|gb|EE073439.1|EE073439
EST:     TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
genomic: TACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA
EST: gi|110405475|gb|EC971016.1|EC971016
EST:     GTCAAGTCCCTGCAGAATCAAGTAGAG                         TTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATTGGACATGAA
genomic: GTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctc ... ttttgggcagTTCCTTGTGGGCAAGCTTGCTTCTATAAGCCCTATGCTGATAGGACATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATTGGCAAGACTCTCGTACTGGATGAGATAATCAACTATGTCAAGTCCCTGCAGAATCAAGTAGAGgtaaaatctcctctccacaccccccaccacatttctatacatttatcaaaccctaaaggtattttttttgaaattttgggcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG