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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttactatcctgtctcctgtcattgttagaacacaagccaaatttaattattctgtttaagtagaagtaaaacataagatgcccaagcattg...

Basic information

species Vitis vinifera
transcript Vv13s0019g01900.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 4
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttactatcctgtctcctgtcattgttagaacacaa--gcca-aatttaatta-ttctgtttaagtagaagtaaaacataagatgcccaagcattg
||||| || ||||||||||| || ||||||||||| ||||||||||||  ||| || || || ||||| || ||  |  |||    |  |   | |||| |    ||  | | | ||  |       | | |||| ||| |  | ||| |  | ||                            
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcag----------------------------

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 5'ss of exon 6
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttactatcctgtctcctgtcattgttagaacacaagccaaatttaattattctgtttaagtagaagtaaaaca---taagatgcccaagcattg
||||| ||||||||||| ||||| ||||||||||| || || || |||||||| ||||| || ||||| || ||  ||||||||    | |   | | ||    |||||| |  || |      |     ||||  ||    ||| ||    ||   |||||        |       ||  |
GTTGGAGAGGTTGCAAAGATCACATGCAAGCCAGAATATGCTTATGGAGCTGCAGGTTCACCTCCAGAGATACCGCCAGAgtaag---tctgaaaacttgat--ctgtcactagtaaagtctttggtttttttatgtacagagttcaaaggtaacagaaacagctctgtttttttttccacag

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G34120.1 (Glycine max), 5'ss of exon 4
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttactatcctgtctcctgtcattgttagaacacaagccaaatttaattattctgtttaagtagaag-taaaacataagatgcccaagcattg------
||||| || ||||||||||| |||||||||||||| || ||||| ||   ||| || ||||| |||||||| ||| ||||||| |||| | |     |  |    |||     |   |||| ||     |   ||  ||   ||| ||  | ||  |   | | ||  |   | ||  ||       
GTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGAgtactattctcatgccacaattatttgtt----tggaaacataattatgaagcaaaaat---gttcaaaaataacctgggatacaaattctactagtgttctaatta

upper sequence: Vv13s0019g01900.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G04170.1 (Glycine max), 5'ss of exon 4
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttact------atcctgtctcctgtcattgttagaacacaagccaaatttaattattctgtttaagtagaagtaaaacataagatgcccaagcattg
 |||| || ||||||||||| |||||||||||||| || ||||| ||   ||| || ||||| |||||||| ||| ||||||| | || | |        ||  ||| |     |||  |||  | ||||   || || || |||     |    || || |   ||    | |  | ||  ||  
-TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaa-aagttcaaatatcaacctgggatacaaattctactggtgtt--ctaattat--

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|28967033|gb|CB346066.1|CB346066
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110697869|gb|EE075334.1|EE075334
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110366799|gb|EC930717.1|EC930717
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|71877473|gb|DT026528.1|DT026528
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|351029576|gb|FQ427416.1|FQ427416
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|351024603|gb|FQ433018.1|FQ433018
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|22015347|gb|BQ800381.1|BQ800381
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110418060|gb|EC984172.1|EC984172
EST:     GGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: GGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|77587550|gb|DV222939.1|DV222939
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110376394|gb|EC941458.1|EC941458
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110415144|gb|EC981021.1|EC981021
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|28967261|gb|CB346294.1|CB346294
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110417551|gb|EC983617.1|EC983617
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|110422056|gb|EC988368.1|EC988368
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
EST: gi|30302283|gb|CB979077.1|CB979077
EST:     CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGA                         TGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG
genomic: CCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttt ... tttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttactatcctgtctcctgtcattgttagaacacaagccaaatttaattattctgtttaagtagaagtaaaacataagatgcccaagcattg

- - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagtaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtaaaa