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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaacatctttatttttattttttataaatagaagttagtcaaacatcttgattatcatttgtgctttttatatccatatttcatgaagtttat...

Basic information

species Vitis vinifera
transcript Vv19s0090g00580.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 4
GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaacatctttatttttattttttataaatagaagttagtcaaacatcttgattatc-atttgtgctttttatatccatatttcatgaagtttat-----
|| ||||| ||||||||||| || |||||||| |||||||||||||| ||||||| |||      |||  |   || |  |||  | |   ||  ||||   || |  |   |||   |||  ||   |||| |  | | |||||    | |       
GTCATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATTGACAAAAAGAAgtcagt------tctcaaccattttacttttaagaataaatctagtgccactttatctctatttgttttggcaagttatgttgacacttcattttttatgctgctg

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os04g53240.2 (Oryza sativa), 5'ss of exon 5
GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagt---caaacatctttatttttattttttataaataga-agttagtcaaacatcttgattatcatttgt--gctttttatatccatatttcatgaagtttat
|| ||||| ||||| |||||||||||||| || |||||||| |||||||| |||| |||   ||| ||| |        ||    | || ||    | ||||| |  |   |  |     |   |   |  | || | |  |  |   || ||      
GTGATTGTTGAGAAAGCTGAAAGAAGTGATATTCCTGACATCGACAAGAAAAAgtcagtttccaagcatttacgaaaccatagcatttagatttttatttagttagtctattgaaccgctaaaggaaggaatattgtctttaattgctatcaa------

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G076826_T02 (Zea mays), 5'ss of exon 5
GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtca--aacatctttatttttattttttataaatagaagttagtcaaacatcttgattatcatttgtgctttttatatccatatttcatgaagtttat--
|| ||||| ||||||||||| || |||||||| |||||||| |||||||| |||| |||    ||| | | ||  || ||  |   |  |||   | ||  || | || || ||  |||  |||   || |   |  ||      |||  ||| |  
GTGATTGTTGAGAAGGCTGAGAGGAGTGACATTCCTGACATCGACAAGAAAAAgtcagttctcaacttttctaagttaatcataagttcataactgctatacagatatgttcatcttcaaatgt---ttatgagttaatgcca-gtgagatttctac

upper sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S209_115V6.2 (Physcomitrella patens), 5'ss of exon 3
-----------------------------------------------GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaacatctttatttttattttttataaatagaagttagtcaa--acatc-ttgattatca--tttg---tgctttttatatccatatttcatga--agtttat--------------------------------------------------------------------
                                               || || ||||||||||| || | ||| |||||||| ||||| |||||||||||||  |||   |   |   |||||   |||    | |   ||   ||        || | || ||| |  ||||   ||| || |     | | |||  | |  | |  ||                                                                    
AGGCAGAAGCTTCAAGGATCCGTGGCAAGTACCCTGACAGAATTCCAGTGATCGTGGAGAAGGCGGAGAAAAGCGACATACCAGACATCGACAAGAAGAAgtgggtc---cccgtcgctttttgcgtttcgagattgagaggctgttggtggtgtcgtcgagtattaggtttgggatgcgttgtgatcacgtgtttggtcactaatccatgtccctgcaacagaagcatggctgtgtagagtgcggatacggagagtaacgtggaaaggtgtgcgcag

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|27584174|gb|CB006869.1|CB006869
EST:     GAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: GAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110407776|gb|EC973391.1|EC973391
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|32459630|gb|CD800804.1|CD800804
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110390932|gb|EC955876.1|EC955876
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110694887|gb|EE072272.1|EE072272
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|46911389|gb|CN546764.1|CN546764
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110421257|gb|EC987552.1|EC987552
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|110422502|gb|EC988827.1|EC988827
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
EST: gi|71888297|gb|DT037352.1|DT037352
EST:     ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAA                         ATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG
genomic: ATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaa ... atcaatgcagATATCTGGTTCCTGCTGATCTGACTGTTGGGCAGTTTGTTTATGTGATCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGTGGAGAAGGCTGAAAGAAGTGACATACCTGACATTGACAAGAAGAAgttagtcaaacatctttatttttattttttataaatagaagttagtcaaacatcttgattatcatttgtgctttttatatccatatttcatgaagtttat

- - - GTGGAG
- - -  TGGAGA
- - - - GGAGAA
- - - - - - - - -  AAAGAA
- - - - - - - - - - AAGAAG
- - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatagaa