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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 5
gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
               || || |||||  |   ||| |  |   |  |   |    ||| | ||    | |  | ||   ||     ||  | |||   || ||| |  || || ||  || ||||| ||||||||||||||||| ||||| |||||||||||| |  |||| ||||||| ||| ||||  | | ||||||| ||
--------------gttgatactatgtttgctttttataccagtattctcag--aattttttga---tataacttttggcaa----gacatggtaaattt-tatcacttt-tgcagACCATTTCAATATTTTTGTTGGTGATCTTAGCCCAGAGGTTACTGATTCCGCATTATTTGCATTCTTCTCTGGATATTCCAGTTGCTC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 5
gttggtttctgtagtttaatt------ctatgcataagtttcactcttatgctgca---aactgattctatggagttttg-gcattcatcattgttgatgttgtattcttgtatgatg---------ttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
||| |   ||| || | || |      |||  | |   |||     || |  |  |      | |    ||| || | || | ||  ||  ||  |||  || ||  |||   || ||          | || |||||| || || ||||||||||| |||||  |||| || || ||||||||||| ||||||||||  || ||||  |   | | ||| ||
gtttggaactgaagctgaagtgctgaactaatcctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctga-attctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 6
gttggtttctgtagtttaattctatgcataagtttcactcttatgct-gca----aactgattc----tatggagttttg-gcattcatcattgttgatgttgtattcttgtatgatg---------ttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
||| |   ||| || | || |      ||||   |   | ||||  | | |    |  || |||     ||| || | || | ||  ||  ||  |||  || ||  |||   || ||          | || |||||| || || ||||||||||| |||||  |||| || || ||||||||||| ||||||||||  || |||| ||   | | ||| ||
gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctga-attctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 5
gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggag--ttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
            || ||||    |   ||  |    |   | || ||     ||||| || |||    |||||||    ||  |   | || | |  |  ||   |  |  | || |||||||| ||| || |||||||| ||||| || |||||||||||||||||||| |||||||||||||||||||| | ||||||||||||
-----------aagcttaa----acaaatgggccctatgttcatacta-ggcctgatcctttgggaacttttggctaagatattatattatatggcttgtttcctt--taatttgcagGTCACTACAATATATTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGTTGTTTGCATGCTTTTCTGTCTATCCCAGTTGTTC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 5
gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
            | |    ||  |   ||| |    |   | || ||  |  ||||| |        ||||| |    |       | | | |  || || | |  |  | || |||||| | ||||||||||||||| ||||| || ||||||||||||||||||||  ||||||||||||||||||| | ||||| ||||||
-------ataaaaataagcttaaacaaataggacctatgttcatacta-agtctgatccc------ctttgggaacttttggctaaggtatagcctttttcttt--taatttgcagGTCATTACAACATTTTTGTTGGCGATCTAAGTCCTGAGGTTACTGATGCTACGCTGTTTGCATGCTTTTCTGTCTATCCCACTTGTTC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 5
gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
                      || |  |    ||   |    || ||||   || || ||||   |||||    |  |||      ||||| || | |   |||| ||||   |||||| ||||||||||||||||| |||||||| || ||||| |||||||| ||||| | |  | |||||||||| ||| ||||||||||
---------------------gtaagttttgactttttttaagtgttgcattttgtttgtatgt--ttttgaggatactca------atgttttagtttc-catga-gttgc--agGTCATTTCAACATTTTTGTTGGAGATCTCAGTCCAGAGGTCACTGATGCAACATTATATCAAAGCTTTTCTGTCTTTTCCAGTTGTTC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 5
gttggtttctgtagtttaattctatgcataagtttcactcttatgctgcaaactgattctatggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
               | | ||||    || ||      |    ||      |||  |||| |    | || |  |    ||| ||      ||  || | || | |||   || |||||| ||||||||||||||||| ||||| || || ||||||||||||||  |||||||||   ||||||||| ||||  ||| || ||
--------------gtaagttct---tatgagcacggattgattgtcaaggact--ttctttttgttctttgagtgaggcatggtactgaatg-gttttggtttcatgaaatgcagGTCATTTCAACATTTTTGTTGGAGATCTTAGTCCAGAGGTTACTGATGCAGCATTGTTTGATAGCTTTTCTGCTTTTAACAGCTGCTC

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|161716028|gb|FC065534.1|FC065534
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGTACACTTCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|349811318|gb|FQ407544.1|FQ407544
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|161705670|gb|FC055790.1|FC055790
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACTTCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|161721264|gb|FC069684.1|FC069684
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|110694202|gb|EE071104.1|EE071104
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACTTCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|110696392|gb|EE072470.1|EE072470
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACTTCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|351031018|gb|FQ439054.1|FQ439054
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|161707025|gb|FC055133.1|FC055133
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACTTCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|27755123|gb|CB035878.1|CB035878
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTG
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTG
EST: gi|77582239|gb|DV220083.1|DV220083
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACTTCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
EST: gi|110357183|gb|EC920553.1|EC920553
EST:     TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG                         GTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA
genomic: TATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAGgttggtttct ... tgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagttttggcattcatcattgttgatgttgtattcttgtatgatgttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC
                     tgttgat  putative branch site (score: 4)
                             ttgtatt  TA-rich tract