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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTAGCCATGGAGTCTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttcttaattttcttttatggttcactacctgcctcttcatgttctagccctttttttttagcatatgctactttgaaatatgtatatttgatt...

Basic information

species Vitis vinifera
transcript Vv04s0023g00780.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g00780.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
TGTTAGCCATGGAGTCTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttcttaattttcttttatggttcactacctgcctcttcatgttctagccctttttttttagcatatgctactttgaaatatgtatatttgatt
|  | || |||||||| ||||| |||||||||  ||||||  | ||||||||||| |||||||||||||   ||    ||| |    ||   ||   |   |  | ||    |   ||      |  | | | | | || || ||  |  | || | |       
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaa--atttgacattgtggactaaattttcgtggatatcact----gaggtaattagatgatctgatcgt-tgttattt--atttgtgcacag------
















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|110407584|gb|EC973189.1|EC973189
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
EST: gi|349823710|gb|FQ415121.1|FQ415121
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
EST: gi|110724898|gb|EE101128.1|EE101128
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
EST: gi|351016199|gb|FQ435519.1|FQ435519
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
EST: gi|30320767|gb|CD004029.1|CD004029
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
EST: gi|110423364|gb|EC989709.1|EC989709
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG
EST: gi|33409355|gb|CF214982.1|CF214982
EST:     TCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTTGAAG-ATCNG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGA
genomic: TCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAA-Ggtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGA
EST: gi|351057151|gb|FQ450858.1|FQ450858
EST:     CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAGGCTTGAAG
genomic: CTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttc ... tctttcacagTTTGCATTGCTGGAGAGTTCTTCAGTTGATGATGATCTTGCAAGCTTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTAGCCATGGAGTCTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttcttaattttcttttatggttcactacctgcctcttcatgttctagccctttttttttagcatatgctactttgaaatatgtatatttgatt

- - - - - - - -  CAAGCT
- - - - - - - - - AAGCTG
- - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA