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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTCAGGAGACATGGGGACATCATTAAGAGGACTGTAGGAGGCTATTTTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacattcttctcagtcctttctctcttttgtaagtgctcatgatgtaagttacaagcttactcaatagccaatgagcctgccatatgccacaaggt...

Basic information

species Vitis vinifera
transcript Vv06s0004g00750.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00750.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA08G11980.1 (Glycine max), 5'ss of exon 12
CACCTCAGGAGACATGGGGACATCATTAAGAGGACTGTAGGAGGCTATTTTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacattcttctcagtcctttctctcttttgtaagtgctcatgatgtaagt-tacaagcttactcaat-agccaatgagcctgccatatgccacaaggt
   || ||||||||||| || || || || || ||||| |||||| ||||||||||||||||  | ||||||||||| |||||| |||| || || |||||| | |||  | | |  |  ||| | | | | |        |||     |  | |||    ||  | ||| ||| ||  |       ||||      |  |
GTTCTTAGGAGACATGGAGATATAATCAAAAGAACTGTTGGAGGCCATTTTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatcatccactata-tttatgtttatagctc-catccatctcccagttctactcttttttttaatcagctaaaaaatgattgatatatatatatat

upper sequence: Vv06s0004g00750.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA05G29030.1 (Glycine max), 5'ss of exon 12
CACCTCAGGAGACATGGGGACATCATTAAGAGGACTGTAGGAGGCTATTTTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacattcttctcagtcctttctctcttttgtaagtgctcatgatgtaagttacaagcttactcaatagccaatgagcctgccatatgccacaaggt-------
   || ||||| || || || || || || || || || |  || ||| ||||||| ||||| || ||||||||||||||||||||||| || || |||||| ||  |  | |   |      ||   ||    |   ||| || | | |  | | |   |     | ||  |||  |||   | |   |  |    ||       
ATTCTTAGGAGGCACGGAGATATAATAAAAAGAACAGTTGATGGATATATTGTTGTGCAAGGGAGGGCTGATGACACCATGAATCTTGGTGGAATAAAGgtatcat-tattacatggaaacaactgaatt----agaagctaatcaggaatttcaaagattctgatagtaatcaa--agctatcaacgagggaagcagtagaagaa

upper sequence: Vv06s0004g00750.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT1G55320.2 (Arabidopsis thaliana), 5'ss of exon 12
CACCTCAGGAGACATGGGGACATCATTAAGAGGACTGTAGGAGGCTATTTTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacattcttctcagtcctttctctcttttgtaagtgctcatgatgtaagttacaagcttactcaatagccaatgagcctgccatatgccacaaggt--
|  || || ||||| || |||||  | ||| | ||||| ||||| ||||    ||| ||||| ||||||||||| |||||||| ||||| ||||| ||||||| |||| | |   |   || | |  |      || | |    |||   ||||  ||  || |||||      ||         || ||  | || |   
CGACTTAGAAGACACGGTGACATTGTGAAGCGAACTGTTGGAGGATATTACAATGTTCAAGGTAGAGCTGATGATACCATGAACCTTGGAGGCATTAAGgtactacatacattgtatgtctatataccc-----aacttc----gattagagttggaacttttctcaagttttcatcttttgtttatctgttataacgcag

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|110712126|gb|EE089391.1|EE089391
EST:     TTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAG                         ACNAGTTCAGTTGAAATTGAACGTGTGTGTGAACA-GGCTGATGAAAGTGT
genomic: TTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacatt ... tgatatgcagACAAGTTCAGTTGAAATTGAACGTGTGTGTGA-CAAGGCTGATGAAAGTGT
EST: gi|110701331|gb|EE078783.1|EE078783
EST:     TTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAG                         ACAAGTTCAGTTGAAATTGAACGTGTGTGTGACAAGGCTGATGAAAGTGTT
genomic: TTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacatt ... tgatatgcagACAAGTTCAGTTGAAATTGAACGTGTGTGTGACAAGGCTGATGAAAGTGTT
EST: gi|110732964|gb|EE108721.1|EE108721
EST:     TTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAG                         ACAAGTTCAGTTGAAATTGAACGTGTGTGTGACAAGGCTGATGAAAGTGTT
genomic: TTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacatt ... tgatatgcagACAAGTTCAGTTGAAATTGAACGTGTGTGTGACAAGGCTGATGAAAGTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCTCAGGAGACATGGGGACATCATTAAGAGGACTGTAGGAGGCTATTTTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacattcttctcagtcctttctctcttttgtaagtgctcatgatgtaagttacaagcttactcaatagccaatgagcctgccatatgccacaaggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctctc