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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTATCTGTCGGTGGGCTGTGGACCTGTGGTTTCGGTATTTCATCGTTAGCGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctctgatcctcggttctgttttactttcgaagtcatcttccgaattactcattttctgtttggttgccaagaaaacgatggaaaaacgaatgaa...

Basic information

species Vitis vinifera
transcript Vv06s0004g04800.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 1
TTTATCTGTCGGTGGGCTGTGGA-CCTGTGGTTTCGGTATTTCATCGTTAGCGGTTTG--AAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctctgatcctcggttctgttttactttcgaagtcatcttccgaattactcattttctgt-ttggttgccaagaaaacgatggaaaaacgaatgaa---------------------
    ||          || ||   |||  | |  | | |        |  ||| |      |     |  || ||||| ||| ||||||||||||||||||||||| || |     || | |  ||  |   ||  | ||  ||  ||||| || |  |     |  |  || |     |  |  |   ||    |   |||                       
---CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc--cccccagcactagtcgtctcac-aatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcag

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g62420.5 (Oryza sativa), 5'ss of exon 1
TTTATCTGTCGGTGGGCTGTGGA-CCTGTGGTTTCGGTATTTCATCGTTAGCGGTTTGA--AAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctctgatcctcggttctgttttactttcgaagtcatcttccgaattactcattttctgt-ttggttgccaagaaaacgatggaaaaacgaatgaa--
    ||          || ||   |||  | |  | | |        |  ||| |      |     |  || ||||| ||| ||||||||||||||||||||||| || |     || | |  ||  |   ||  | ||  ||  ||||| || |  |     |  |  || |     |  |  |   ||    |   |||    
---CTCCACGAAAACCCTCTGCCTCCTTCGCTCGCTGCACCCTCGTCTCGGCGATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc--cccccagcactagtcgtctcac-aatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgct

upper sequence: Vv06s0004g04800.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA13G41120.1 (Glycine max), 5'ss of exon 1
-TTTATCTGTCGGTGGGCTGTGGACCTGTGGTTTCGGTATTTCATCGTTAGCGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctctgatcctcggttctgt-tttactttcgaagtcatcttccgaattactcattttctgtttggttgccaaga---aaacgatggaaaaacgaatgaa
 ||| ||| ||  |   || ||      |  |  |  | | || |    | ||     ||  ||||| ||||| || ||| |||| ||||||||||||||||||||| ||     ||   |||    ||||| ||     |  | ||  | ||  |   ||||   |||  |  | | ||   |||    || |   | | |   
GTTTCTCTTTCTCTTT-CTCTGTCTGCTTCTTCACTTTCTCTCGTTTCAATCGAAAAAAATCATGGGCAGAAAATTCTTCGTCGGTGGCAACTGGAAATGCgtatgtttcaatcactatcttcaccatttacctttt---tttttttttgcatgtccggtttttgttttaatctcgatgagtgaaatctcggtagttctactct-

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|110415564|gb|EC981483.1|EC981483
EST:     CGGTTTGAAAAATGGGGAGAAAGTTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|351028511|gb|FQ444792.1|FQ444792
EST:     AAAGTTTTTCATCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: AAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|30129525|gb|CB914864.1|CB914864
EST:     CGGTTTGAAAAATGGGGAGAAAGTTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|294965195|gb|GW837026.1|GW837026
EST:     CGGTTTGAAAAATGGGGAGAAAGTTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|110692722|gb|EE068329.1|EE068329
EST:     CGGTTTGAAAAATGGGGAGAAAGTTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|349826936|gb|FQ419027.1|FQ419027
EST:     AAAGTTTTTCATCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: AAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|161710111|gb|FC059796.1|FC059796
EST:     GAAAAATGGGGAGAAAGTTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: GAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|71871008|gb|DT020063.1|DT020063
EST:     AAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: AAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|294963951|gb|GW836826.1|GW836826
EST:     CGGTTTGAAAAATGGGGAGAAAGGTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTCGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|161720486|gb|FC070598.1|FC070598
EST:     TTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: TTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|87586476|gb|DY474727.1|DY474727
EST:     CGGTTTGAAAAATGGGGAGAAAGTTTTTCGTCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
EST: gi|161714171|gb|FC062916.1|FC062916
EST:     CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGC                         AATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT
genomic: CGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctct ... atcaatgcagAATGGAACAGTTGAGGAGGTGAAGAAGATTGTTACTGTTTTGAATGAGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTATCTGTCGGTGGGCTGTGGACCTGTGGTTTCGGTATTTCATCGTTAGCGGTTTGAAAAATGGGGAGAAAGTTTTTCATCGGCGGCAACTGGAAATGCgtatgtctctgatcctcggttctgttttactttcgaagtcatcttccgaattactcattttctgtttggttgccaagaaaacgatggaaaaacgaatgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaa