Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggattaaaaataataaaaataaaaataaacttggtttcattttagaccataaatttcatattttactcagtttatgacttgcattttgaaatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG

Basic information

species Vitis vinifera
transcript Vv18s0117g00150.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0117g00150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g23120.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------cggattaaaaataataaaaataaaaata--aacttggtttcattt--tagaccataa---------atttcatattttactcagtttatgac-ttgcat--tttgaaatgga----gcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG
                                                                                  | | || |  || || | || |||  |       ||| |||   | |  |||          ||| | | | | |||| ||||||  | |  |||  ||  |  || |    ||||||||| ||||| ||||| |||||||| ||  |||  |     || |||||||| || ||||| |||||||||||||||||||||||| |  | |  ||||
gtaaattgtttgattcctgttgctacctgacttcttttgatcctttgagcttggttgtatgaatgtcggttaccagagtatgtcataagtt-tataagttaatatactagtccaacttcctttagcaaaaaataggcattgcctattgcttctctcactctgtttatatcgtaacatgattcaacgtgaaacatgcagGTTGAAATTAAGAGAACTATTCCAAAGGGTGCTGCCCCCCTAAAAGATTTCAAGACGAAGAAAATATTTGTTGGTGGATTACCATCTGCTTTGAAAGAAG

upper sequence: Vv18s0117g00150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G152526_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------cggattaaaaataataaaaataaaaataaacttggtttcattttagaccataaatttcatat-tttactcagttt---atgacttgcattttgaaatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG
                                            | |  | |    |||  | || |   |  ||        ||  || || ||||    |   | |||    |||||   ||| | |  | | | |||||   |||||||| ||||| ||||| || || || ||  ||| ||  | ||| |||||||| || |||||||| ||||||||||||||||| ||  |  | |  ||||
gtaaactttttggttttgtctttggtttatatctttgtctcactctgtattagctcaatgtacatcatgtttcacgaaaacatatagtaaacaataagaagcgcttgtttgtgtagtttgaaatgtcatttactctaaaatg---cagGTTGAAATTAAGAGAACGATCCCTAAGGGAGCTGCTCCTTTGAAAGATTTCAAGACGAAGAAGATTTTTGTTGGTGGATTACCCTCAGCTCTAAAAGAAG
















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|33407717|gb|CF213344.1|CF213344
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|110712411|gb|EE090004.1|EE090004
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|110719186|gb|EE096875.1|EE096875
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|71873142|gb|DT022197.1|DT022197
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|161721778|gb|FC071127.1|FC071127
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|161706369|gb|FC055475.1|FC055475
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|37188093|gb|CF607444.1|CF607444
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|351030617|gb|FQ437043.1|FQ437043
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|351027170|gb|FQ440038.1|FQ440038
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|110710940|gb|EE087573.1|EE087573
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAGGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|351014903|gb|FQ438103.1|FQ438103
EST:     CAGTTGTCGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|351039455|gb|FQ461322.1|FQ461322
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
EST: gi|110707058|gb|EE083127.1|EE083127
EST:     CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAG                         GTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC
genomic: CAGTTGTTGACAGTGTCATTGAAGATACACATGTTATTAACGGAAAACAGgtaaagcatc ... aatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccataaatttcatattttactcagtttatgacttgcattttgaaatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG
     taaatttcatatttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggattaaaaataataaaaataaaaataaacttggtttcattttagaccataaatttcatattttactcagtttatgacttgcattttgaaatggagcagGTTGAGATTAAAAGAACCATTCCAAAAGGCTCTGGTCAATCGAAGGATTTCAAAACAAAGAAGATATTTGTTGGTGGATTACCATCTACAGTCACTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - aaaaata
- - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - -ccataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg