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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG

Basic information

species Vitis vinifera
transcript Vv16s0022g01770.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 7
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattg-acttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
     ||   | | | |  ||  ||  || |  |   ||     ||||    |  |     | | | | |    |||   ||  | || |  ||| |||  | |  |||||||| ||||||||||||||||||||||||||||||||   | |   |||  | ||||||||  | || ||||||||||||
----gtttgttgagcatacaa--ctggctaaattaatttgatggttatgggctaaggcacttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGA---GGACCAAACCTATGATCTTAACTTCAAGGAAGAG

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 3'ss of exon 10
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
     || | |  | |    ||| ||   | ||| | |  ||| | | |  || |   ||   |||   |  || || | | |   |  ||     ||  | | | ||||||| ||||| ||||||||||||||||| || |||||  || ||||||| || ||||||||| | || |||||||| |||
---gtttgtgtactttgattaatttattgtttatctttctgca-taagttaatgtttttg---attgactgaggcttgagacttttt--ttgcaacctgatatggtagGTTGTCATTGGAATGGATGTTGCTGCTTCGGAATTCTACAATGACAAGGACAAAACCTATGACCTTAACTTCAAGGAGGAG

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G133721_T01 (Zea mays), 3'ss of exon 1
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttatta-tttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
                             ||| ||   |   |  || |    |  ||     |  |   ||||  | || | |   |    | | || | | | |||||| || ||||||||||||||||||||||| |||||||  | | | || || ||||| |||||  | ||||||||||| |||
----------------------------gtatgttctctcttatctacttggctcacaaacagacaaacctttgtgtgtatagttgatt-caacttacatgtgtggcagGTGGTCATTGGGATGGATGTTGCTGCTTCTGAGTTCTTCGGTGAGAAAGACAAGACTTATGATCTTAATTTCAAGGAGGAG

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G064302_T01 (Zea mays), 3'ss of exon 10
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttt-tggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
                             ||| ||   |   |  || |    |  ||     |  ||  | ||  | |  | ||  |    | | || ||| | |||||| || ||||| ||||||||||||||||| |||||||  | | | || || ||||| |||||  | ||||||||||| |||
----------------------------gtatgttctctcttatctacttgcctcacaaacagacaatcctatgtgtgtgtagtcgatt-caacttacctttgtggcagGTGGTCATTGGAATGGATGTTGCTGCTTCTGAGTTCTTCGGTGAGAAAGACAAGACTTATGATCTTAATTTCAAGGAGGAG

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 10
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
                            ||  || | |    ||| | |||| ||       || ||| ||      ||      ||||||| |  || ||||| ||||||||||||||||||||||||||||||||||| || || |||||||||||||| ||||||||||||||||| |||||||||
---------------------------gttgaatctttgtctactgaatctaatt-------tagtatcttataacatatg---gctgattagtttctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG

upper sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G28100.1 (Glycine max), 3'ss of exon 10
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttg-gttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
                            ||   |||      ||| | |||| ||       ||| || ||    | ||| |||  ||||||| |  || ||||| ||||||||||||||||||||||||||||||||||| || |||||||||||||| || ||||||||||||||||| |||||||||
---------------------------gttgagttttcgtctactgagtctaatt-------tatcatcttaatatattatatt-gctgattaatttctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTATGATAACAAGGACAAAACCTATGACTTGAATTTTAAGGAAGAG

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|26264399|gb|CA815462.1|CA815462
EST:     CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATTACTGGAAAG                         GTTGTAATTGGGATGGATGGTTGCTGCTTCAGAGTTCTATGATAACAAGGA
genomic: CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATAT-ACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATG-TTGCTGCTTCAGAGTTCTATGATAACAAGGA
EST: gi|34546318|gb|CF514550.1|CF514550
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATGATCN-GGA
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAA-CAAGGA
EST: gi|110716823|gb|EE092142.1|EE092142
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|27586582|gb|CB009277.1|CB009277
EST:     CTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: CTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110718521|gb|EE095450.1|EE095450
EST:     CCTTGAACTACTGGAGAAAGCTTATTGCAAAA-CTGGATATACTGGAAGG                         GTTGTA-TTGGG
genomic: CCTTGAACTACTGAAGACAGCT-ATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGG
EST: gi|156732544|gb|EV236665.1|EV236665
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|161720244|gb|FC070896.1|FC070896
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110720665|gb|EE096796.1|EE096796
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|161719189|gb|FC069366.1|FC069366
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|30306211|gb|CB983005.1|CB983005
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGAT
EST: gi|110422151|gb|EC988464.1|EC988464
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGAAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|27585372|gb|CB008067.1|CB008067
EST:     CTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: CTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110405512|gb|EC971053.1|EC971053
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110718366|gb|EE095119.1|EE095119
EST:     C-TTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATTACTGGAAAG                         GT-GTAANTGGG
genomic: CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATAT-ACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGG
EST: gi|30299610|gb|CB976404.1|CB976404
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGAT
EST: gi|27584827|gb|CB007522.1|CB007522
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|30305096|gb|CB981890.1|CB981890
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110715456|gb|EE093529.1|EE093529
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|30297175|gb|CB973969.1|CB973969
EST:     GCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|30297322|gb|CB974116.1|CB974116
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110720119|gb|EE095760.1|EE095760
EST:     CCTTGAACTACTGAAGACAGCTATTGGCAAA-GCTGGATATACTGGGAAG                         GTTGTATTTGGGATGGA
genomic: CCTTGAACTACTGAAGACAGCTATTG-CAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGA
EST: gi|30301049|gb|CB977843.1|CB977843
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|34548818|gb|CF517050.1|CF517050
EST:     CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAANGAT
genomic: CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGG-ATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|33408905|gb|CF214532.1|CF214532
EST:     CCTTGAACTACTGATGACAGCTATTGCAAAAGCTGGATATACTGGAAAAG                         GT-GTAATTGGGATGGATGTTTGCTG
genomic: CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAA-Ggtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTT-GCTG
EST: gi|110718755|gb|EE095948.1|EE095948
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GT-GTAATTGG
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGG
EST: gi|110686170|gb|EE063531.1|EE063531
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|30305283|gb|CB982077.1|CB982077
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|161719251|gb|FC068252.1|FC068252
EST:     GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
genomic: GCCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGAAAGgtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGAT
EST: gi|110713035|gb|EE088603.1|EE088603
EST:     CCTTGA-CTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGGGAAAG                         TTTGTA-TTGGG
genomic: CCTTGAACTACTGAAGACAGCTATTGCAAAAGCTGGATATACTGG-AAAGgtaacttctc ... tttcttgcagGTTGTAATTGGG
EST: gi|110362047|gb|EC925554.1|EC925554
EST:     AAAAGCTGGATATACTGGAAAGG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGA
genomic: AAAAGCTGGATATACTGGAAA-Ggtaacttctc ... tttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatggttattatttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG
                                     tattgac  putative branch site (score: 2)
                                           cttttcttgc  CT-rich tract
        ttattatttttggttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA