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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctgatctggcttttgtaaattctcttacccaatctaattgtatccccactacaaattacagctgcattcttaggtttccgcggatctttc...

Basic information

species Vitis vinifera
transcript Vv18s0122g00090.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00090.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os07g39280.1 (Oryza sativa), 5'ss of exon 1
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctgatctg---gcttttgtaaattctcttacccaatctaattgtatccccactacaaattacagctgcattcttag----gtttccgcgg-atctttc-----------------------------------------
||||| || || || ||||| ||||| ||  ||||||||||||| || |||||||| ||||||||||| |||||| ||   || ||||| |||  |||||||     || |   |  |   |||  |     | | ||| |||  |||      |||   |     |  | | | |   ||| | |    |   |||||| ||||                                            
TCCGACGTCGGGGCGTGGGCGATGAACGTCGTCAGCTCCGTCGGCATCATCATGGCAAACAAGCAGCTCATGTCCTCCTCCGGCTACGCCTTCTCCTTCGgtacccttcgcgccttcgcgcgctcctcctcctcccctttcccc-tctccgcagatctggatccgcaggttcgggtttgttcctggtgacgccgccgcgggatctgattttttcttctttttttcgtttcctcctttggtcgaatgcag

upper sequence: Vv18s0122g00090.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA11G00210.2 (Glycine max), 5'ss of exon 1
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctgatctggcttttgtaaattctcttacccaatctaattgtatcccc-actacaaattacagctgcattcttaggtttccgcggatctttc-------
|| |||||||| || ||||||||||| ||| ||||||||||||||||||| ||||| ||||| ||||||||||||  || ||| || || |||||||| ||| |||||||||  |||  |   | | | ||||||     |   |  ||| |||    |||   | | | || |    ||| |  | | ||    ||| |        
TCTGATGTGGGAGCATGGGCCATGAACGTTGTCAGCTCCGTCGGAATTATTATGGCCAACAAACAGCTTATGTCCAACAATGGCTATGCTTTCAGCTTTGgtcagtctctctcttct--caactattatttctctatgtta---tgtttggatctgagactgggagtaatagat---ctctaatttcttcgacattctcttgcatact

upper sequence: Vv18s0122g00090.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA01G45700.1 (Glycine max), 5'ss of exon 1
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctgatctggcttttgtaaattctcttaccc--aatctaattgtatccccactacaaattacagctgcattct--taggtttccgcggatctttc
|| |||||||| || ||||||||||| ||| ||||||||||||||||||| ||||| ||||| ||||||||||||  || ||| || || |||||||| ||| || ||||||  |||    | | |    | | |    |  |  || |  |||      || | |||| |  |  ||||||  |   |||    || |||   
TCTGATGTGGGAGCATGGGCCATGAACGTTGTCAGCTCCGTCGGAATTATTATGGCCAACAAACAGCTTATGTCCAACAATGGCTATGCTTTCAGCTTTGgtcagcctctctcttctcaactctatgttatgtttggatctgagactgagagtaatagatct-ctaatttcttcgacattctcttgcatttttatggttct---

upper sequence: Vv18s0122g00090.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G76670.1 (Arabidopsis thaliana), 5'ss of exon 1
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctga-tctggcttttgtaaattctcttacccaatctaattgtatccccactacaaattacagctgcatt-cttaggt-ttccgcggatctttc
|| ||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||||||||| || ||||| |||||  ||  ||||| ||  ||  |||| |||  | ||||||   |||| || |  |  ||     | ||  ||    ||  |  |    |  |  | ||   | | ||  |||  | |||| | |       
TCTGATGTCGGTGCATGGGCTATGAATGTAATCAGCTCCGTTGGAATCATCATGGCTAATAAACAGCTCATGTCTTCCTCTGGTTTCGGTTTTGGCTTTGgtatgcctctctctctctgactctgatctatctatctccc--attagcttacacacttcatgaatctgacgatttctttgtttatatattccacag-------

upper sequence: Vv18s0122g00090.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S116_49V6.1 (Physcomitrella patens), 5'ss of exon 2
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct---ctgatctggcttttgtaaatt--ctcttacc-------------caatctaattgtatccccactacaaattacagctgcattcttaggtttccgcggatctttc---------------------------------------------------------------------------
|| |||| ||| || |||||||||||||| |||||||| || ||||| |||||||||||||||||| | ||||| ||   ||| || |  ||  | || ||| ||   |    ||         |||||| ||    ||||||                |  |  | | |  | | |||| |  | ||   ||  |||      | |  ||||  |                                                                             
TCTGATGCGGGCGCATGGGCCATGAATGTAATCAGCTCTGTTGGAATCATCATGGCTAACAAGCAGGTCATGTCGGCAGCTGGCTATGACTTTCGGTTTGgtgagatcccgagcttgcagaaactttgtacatcagttcttactatcagaagagagattacttggtcgaagtctcgctacgacattcaagagctgtctgtaaccttcagggataataggagttcccatacgtgtcagcaaacgtaatgagctttttcttttttctgattattttgctgaattatgttgtgcag

upper sequence: Vv18s0122g00090.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S15_388V6.3 (Physcomitrella patens), 5'ss of exon 2
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctgatctggcttttgtaaattc---tcttacccaatctaattgtatc-cccactacaaatta--cagctgca--ttcttaggtttccgcggatctttc------------------------------------------------------------------------------
|| |||||||| || |||||||||||| |||||||||| || || |||||||||||||| || ||  |||||||     | |||||||  ||||| || ||| ||  |    || |    | | |  |  ||    | | | |    |  ||    |      |||  |  |  ||| ||||    || |||||  ||| |     |                                                                               
TCAGATGTGGGAGCTTGGGCCATGAATATTATCAGCTCTGTTGGTATTATCATGGCTAATAAACAAGTTATGTCGAAAGGAGGTTACGACTTCAGATTTGgtgaggtttcacgagccacatatggcgatctcgaaccatgctcgtgtttctttcgccgtttgttacctacgattcagttgcaaaccctcaggttgacgcagtagggtaatggacctgggatttatagccattggatgttcattgcatgaattccatcttctcttactggctaattcctggatgcag

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|71863220|gb|DT012275.1|DT012275
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|352763513|gb|FQ473216.1|FQ473216
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|18458909|gb|BM437187.1|BM437187
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|352764235|gb|FQ471215.1|FQ471215
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|294965571|gb|GW837170.1|GW837170
EST:     ATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCAATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: ATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCA-TTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|351015703|gb|FQ427188.1|FQ427188
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTAGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|349822122|gb|FQ412386.1|FQ412386
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|33406641|gb|CF212268.1|CF212268
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|30321629|gb|CD004891.1|CD004891
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|351014386|gb|FQ437388.1|FQ437388
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|349829126|gb|FQ419658.1|FQ419658
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|349808132|gb|FQ403319.1|FQ403319
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
EST: gi|349826092|gb|FQ415897.1|FQ415897
EST:     CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCG                         CCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG
genomic: CATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctct ... tctttttcagCCACCACTTTAACTGGGTTTCATTTTGCGGTTACTGCACTGGTTGGTCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGATGTGGGTGCCTGGGCCATGAATGTTATCAGCTCCGTCGGAATTATCATGGCTAACAAGCAGCTTATGTCCGCCAGTGGTTACGCATTCAGCTTCGgttagtctctctgatctggcttttgtaaattctcttacccaatctaattgtatccccactacaaattacagctgcattcttaggtttccgcggatctttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccccac