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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caggagaataaaagaaatgctatataagatagtacaacattctagtaatagggaaactaccacctctaactgctttacttgttggatggttggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA

Basic information

species Vitis vinifera
transcript Vv11s0016g02850.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------caggagaataaaagaaatgctatataagatagtacaacattctagtaatagg--gaaactaccacctctaactgctttacttgttggatggttggtc-tgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA
                                                            ||  |  |      || |     || || |   |  |  || || |  |  |  |||| |   |    ||   || ||| | ||||| || || ||  ||||| | || | |||  |||||||||||||  | || || ||||||||||||||||||||||||||||| || |||||||| ||||||  ||   || ||||| 
gtgagttcgcatagaaatgatttatttgttaaaaatgtagagaatttaaacttttcaattcaaaattagttttcaagtttatgattaggtga-atgaatttgtaattttgagtagaaaattatagaattaggagcattaat-gttggttgctttgttatgcagAGGATCACTGAGGGACAGAACAAAGTGATAATTACTGATAGAATGTGGGCTAGGCTTCTGTCTTCAACAAATCAGCCCAGCTTTACGATTGCT-AAGACT

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------------------------------------------caggagaataaaagaaatgctatataagatagtacaacattctag---taatagggaaactaccacctctaactgctttacttgttggatggttggtc-tgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA
                                                                                                ||     |      || |     ||  | |   || |  || ||    | |   ||||| ||     | ||   || |||  |||||| || || ||  ||||| |||| | |||  ||||||| |||||  | || || ||||||||||||||||||||||||||||| || |||||||| ||||||   |   || |     
gtgagttcgttggcctgcttgatattgtcggttctgcttctgcaggatagatatgatttatttgttaagaatgtagtggatttaaacttttcaattcaaagttagttttcaagtttatgattgggtga-acgaagttgtaattttgagtaggaaattatagaatttagaagcatta--tgttggttgctttgttatgcagAGAATCACTGAGGGACAGAATAAAGTGATAATTACTGATAGAATGTGGGCTAGGCTTCTGTCTTCAACAAATCAGCCCAGCTTTACCATTGCTAAGACTG

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA01G00870.1 (Glycine max), 3'ss of exon 12
-----------caggagaataaaaga-aatgctatataagatagtacaacattctagtaatagggaaa--------ctaccacctctaactgctttacttgttggatggttggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA
             | |  |||   |   || | | | || | ||   |    | || |||||   ||         |||| | |  |   || |||  |  || | |  ||| | ||||| |||| | ||| ||||||||| | || |||||||| ||||||||||||||||||||| | ||||| || ||||| || |||||||||    |  | |   
gtgagttcattgggcatgatatttgttgattccacagaataaagatgatttatttattaatattcaataatcctttctactaacatttcatgatttgttgctttgttaattgttatgcagAGAATCACTGAGAGACAGAACCACGTAGTGATAACTGATAGAATGTGGGCTAGGCTTTTATCTTCAACAAATCAACCCAGCTTTTTGGATGCCAAGGGTG

upper sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 12
------caggagaataaaagaaatgct-atataagatagtaca-acattctagtaatagggaaactaccacctctaactgcttt--------acttgttggatggttggtct------gcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA
           |   |  | |  || | ||   | | | || | |   | || | ||    |  | |  |||  |  |||||||        | ||  ||  | |||| | |      |||| |||| |  || ||||||||| | || |||||||| ||||||||||||||||||||| | ||||| || ||||| || |||||||||    |  | |   
gtgagttcattgggcatgacatttgttgattccacagaataaagatgatttatttattaacattcaattacccttttctgctttctactagcatttcatgttttgttgcttttgttacgcagAGAATCACCGAGAGACAGAACCACGTAGTGATAACTGATAGAATGTGGGCTAGGCTTTTATCTTCAACAAATCAACCCAGCTTTTTGGATTCCAAGGGTG

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|46918678|gb|CN548007.1|CN548007
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|110696522|gb|EE072712.1|EE072712
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|30329681|gb|CD012943.1|CD012943
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|29784840|gb|CB341314.2|CB341314
EST:     GTTTACAGTTGGGCCTGTCAATGATC-GACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGAC-GATCNAAGATTGTGATAACAGATAGAATGTGGGC
genomic: GTTTACAGTTGGGCCTGTCAATGG-CAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAG-TTGTGATAACAGATAGAATGTGGGC
EST: gi|161706980|gb|FC057287.1|FC057287
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|33403868|gb|CF209495.1|CF209495
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGGAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|33409346|gb|CF214973.1|CF214973
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|34320835|gb|CF373589.1|CF373589
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|30256405|gb|CB972248.1|CB972248
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|33409425|gb|CF215052.1|CF215052
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTTTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|110363721|gb|EC927331.1|EC927331
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|71884224|gb|DT033279.1|DT033279
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|161705710|gb|FC056619.1|FC056619
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|110361259|gb|EC924720.1|EC924720
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|71882578|gb|DT031633.1|DT031633
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|30256378|gb|CB972221.1|CB972221
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|30256486|gb|CB972329.1|CB972329
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|110361880|gb|EC925383.1|EC925383
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|110729768|gb|EE106084.1|EE106084
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
EST: gi|351045413|gb|FQ447678.1|FQ447678
EST:     GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTAT                         CGAGTTATTGAAGGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT
genomic: GGTTTACAGTTGGGCCTGTCAATGGCAGACATTCTTATATACCTTTCTATgtgagttagc ... tggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatagggaaactaccacctctaactgctttacttgttggatggttggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA
                  ctctaac  putative branch site (score: 2)
                            tttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caggagaataaaagaaatgctatataagatagtacaacattctagtaatagggaaactaccacctctaactgctttacttgttggatggttggtctgcagCGAATTATTGAAAGACAGAACAAAGTTGTGATAACAGATAGAATGTGGGCTAGGCTTCTGTCTTCTACCAATCAGCCAAGCTTTTTGAGCCCTGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - aataaaa
- - - - - - -gaaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - gaaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatgg