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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttgaatctcttttatcatgtaaaggt...

Basic information

species Vitis vinifera
transcript Vv07s0005g03790.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g40830.3 (Oryza sativa), 5'ss of exon 1
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttgaatctcttttatcatg-taaaggt
|| ||||| || || ||||| || || |||||||||||||||||||| ||  ||||||| ||||| ||||||||| | ||  | | |||    || || ||||  |   | |||     |  |   | | ||         |  ||      | | |||     | || |||  |||  | |   ||   ||| ||| || 
AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagttaatgtcagagacttacgaatatattgaacagcagcttgacaagtttctcccagtatgtgcttcagttgtttgttgcttcagatgataatgg-

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G04480.1 (Glycine max), 5'ss of exon 3
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttg-aatctcttttatcatgtaaaggt-
|| |||||| | || || || ||||| |||||||| |||||||| || |||||||| ||||| |||||||||||||||||||||||||| ||  |||||||||||     |    |  | |||| |  | |||      |  |  || || |  ||   |   ||| |||| |  |  ||     | ||  ||   |     
AGTCAAATTTTAGCCGGCGGACGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTGAAGACATAGCTGgtaatgcatgtctcctcctttattcc--tctaattgtgaatttccttcttctcattctatgtccttggttttcaatacaaaactatgtactatagcataaca

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G18730.1 (Glycine max), 5'ss of exon 3
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcatt-ttaacaccataaatttttttttttgtttccttagctttgtttcctttgaatctcttttatcatgtaaaggt
|| |||||| | || |||||  |||| |||||||| |||||||| || |||||||| ||||| |||||||||||||||||||||||||| ||  |||||||||||     |    |  | |||| |  | ||  ||   |    || |  |||| | ||||| |||||   | |    | ||| |  |||    |||    
AGTCAAATTTTAGCCGGTGGAAGAGGTTTGGGAACTTTCAAAAGCGGCCTTAAGGGAGGAGTGCACATTGTTAAGACTGACCAGGTTGAAGACATAGCTGgtaatgcatgtctcctcctttattcctctatttgcattttcttgttctcattttatgtccttggctttcaatacaa-aactctgtactatagcataacatg

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagct--ttgtttcctttgaatctcttttatcatgtaaaggt
||||| ||| | || |||||  ||||  | ||||||||||| ||||||||||||||||| ||||||||||||||   |||  ||| ||| ||| | ||||||| |    |   | | || | | |   |||           ||||| || |||||     || |  |  | |  ||  ||||| | |||   ||||     
AGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtacaggatttcttgtttgtggctttctggagtctgttttttgttgttgttgtacaagttattgatctatttcaaatctttattact-tgtag----

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 5'ss of exon 3
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaa--taaggattgtattttat----atttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttga-atctcttttatcatgtaaaggt
|| ||| | || |||||||| ||||| || || || ||||| | ||| ||||||||||| ||||||||||| ||||  |||||||| |||||| | || ||||         ||  |||||      |  |  || ||      || |    |||  || | |  ||  |||| ||    | |  || |  || ||  | |      
AGTCAAGTGCTGGCAGGTGGTCGAGGGTTAGGTACTTTCAAGAATGGACTTAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctcctttccattttgatagaagctggttctagaggggtagaacaatttggttatgttttt--ctttattagactaggcatgttgttgattctatc-----

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|34545781|gb|CF514013.1|CF514013
EST:     TGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAATATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|110397988|gb|EC964029.1|EC964029
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|30305880|gb|CB982674.1|CB982674
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|110733074|gb|EE108915.1|EE108915
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|71858858|gb|DT007913.1|DT007913
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|161716900|gb|FC064979.1|FC064979
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|71857444|gb|DT006499.1|DT006499
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|294967254|gb|GW840129.1|GW840129
EST:     TAAGGGTGGAGTTCACATTGTNAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAACCTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|71864238|gb|DT013293.1|DT013293
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|110688710|gb|EE067574.1|EE067574
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|30130655|gb|CB915994.1|CB915994
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGTCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|71861252|gb|DT010307.1|DT010307
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGTCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|71856468|gb|DT005523.1|DT005523
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|37187335|gb|CF606688.1|CF606688
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGTCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
EST: gi|161713591|gb|FC062524.1|FC062524
EST:     TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTG                         GCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA
genomic: TAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataagga ... ttttttccagGCAAGATGCTAGGCCAGATCCTTGTCACCAAACAAACTGGCCCCCAAGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttgaatctcttttatcatgtaaaggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accataaa