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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG

Basic information

species Vitis vinifera
transcript Vv09s0002g05800.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 5
-------------------gtagagcccatcatcaacaataacaaaaag--------gaaaaaaaaaatgttgctttctttgt------tgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
                      |||  | ||    | | | | |  |          | ||    || | | | | |   | |      || |||  || ||  ||| | | ||||    |  | |  |||||||| ||||||||||| || || || |||||||| || |||   |||||||||||| | ||||| || |||| |||||| ||||| |||||||||||||| 
gtaaactgagcaaaaataccctgagttcttctattatagtgaaagcattattggcttgcaatctgaactatagttctacatatgcactctgttgtcagtgtaggcttaattgtttggttaacatat--tacagGGAACATGCACCATCCATTATTTTCATGGATGAAATAGACTCCATTGGATCTGCTAGGATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTCCAGCGA

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 4
------------------------------gtagagcccatcatcaacaataacaaaaagga---aaaaaaaaatgttgctttctttgttgctgtttgttta--aactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
                               |  | |  ||  ||||    | |  |||       |     || | ||||| | ||| |      | || |  |   | || | ||    |    || | |||| |||||||||||||| ||||||||||||||||| || |||   |||||||||||| | ||| | ||||||  |||   |||||||||||| || || || 
gtaaacattttctgttgatgatacattgaaatttaccatatattcaatgggatctgaaaatccttcattgggaaggatgcttgcattgctttacactattcagtaggctgacgtctttggtttgaattttgacagAGAGCATGCACCATCCATAATCTTTATGGATGAAATAGACTCCATTGGATCTGCTAGAATGCAGTCAGGATCTGGGGGTGGTGATAGTGAGGTTCAACGC

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 5
----gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
    || |         | ||  ||||        |   | |   ||||  |  |||| |   |||  | |||   |||  | |  |    |   || || |||||| ||||||||||| || || ||||||||||| ||||||  ||| ||||||||| | ||||| || |||| |||||| ||||| |||||||| ||||| 
attagttgtttgtgagttgaagcataattttgcatattcatattctgttattagctttttcattgtgggcttag--tttgttatcgggttcac--ttattgcagGGAACATGCACCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGACAGTGAAGTTCAGCGT

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 5
gtagagcccatcatcaacaataacaaaaa---ggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
  |  |||  |  | |     | || ||    | | |   | ||| |    || | | |   |||  | |||   | |  | | ||    |   || || |||||| ||||| ||||| || || ||||||||||| ||||||  ||| ||||||||| | ||||| || |||| |||||| |||||||||||||| ||||| 
acaaggcct-tagtgagttgaagcataactttgcacatgcacaatctgttattatctttcattgtgggcttagtttgttttatctggttcac--ttattgcagGGAACATGCGCCATCCATTATATTTATGGATGAAATTGACTCTATCGGATCTGCTAGAATGGAGTCTGGAACTGGCAACGGTGATAGTGAAGTGCAGCGT

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 5
-gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
           |||| ||   | |     | |  |     |   |||| |      ||  | | | |  | | | |  |     |  | ||||  | ||||||| ||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| |||||||| ||||||||||| ||||||||||| || ||||| 
aactttttgattcattaattttcatgtttatgttatttggagccttgcctaacc-attattatatatgaatattatcatggaacacttgtcttcttcacagGGAACATGCTCCATCAATTATCTTCATGGATGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAACGGTGATAGTGAGGTACAGCGT

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 5
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtt-tgtttaaactttactttttgaac---tatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
     ||  | | |    | | |  ||     |    |    |   ||| | |      | || | | | ||  ||| || | ||||   | ||||  |  |||||| ||||| |||||||| ||||| ||||| || ||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| || ||||| 
---ttgcttaactttttgattcattaattttcatgttatttggagacttgcctaaccattattatatatgaatatta-ttatggaacacttgtcttcttcccagGGAACATGCTCCATCAATTATCTTCATGGACGAAATTGACAGTATTGGATCTGCTCGGATGGAATCTGGAAGTGGCAATGGTGATAGTGAGGTACAGCGT

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 5
-gtagagcccatcatca-acaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
   || ||| |   |||   ||  |  |||    ||| |     | || || | |||    |  |  ||  |  ||  |||       | | |   || ||||||||||||||||||||| ||||| |||||||| || || |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || || |||
cacagtgccaagtctcatgtaaggagcaaattacaaataggtgagatgatt-cgttgaaaatactctttccag-ttggcttacaccggtttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATTGGGTCTGCTCGTATGGAATCTGGAAGTGGAAATGGTGACAGTGAGGTGCAACGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 5
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactt-tactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
|||  |  ||   |  |||  |  ||  |     |      ||     | |||  || | | | | |||   || || |   |      | |   || ||||||||||||||||||||| ||||| |||||||| || || ||||| || ||||||||||||||||| || ||||| |||||||| ||||| || ||  ||
gtaatgagcaaagtatacaccattaatcatcttcattgtgctgaaaaatactt-attccagctagcttacctttctagtacctctggcttatggttttcagGGAGCATGCACCATCAATCATCTTCATGGATGAAATCGATAGTATCGGGTCTGCTCGTATGGAATCTGGTAGTGGAAATGGTGACAGTGAGGTGCAAAGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S245_17V6.1 (Physcomitrella patens), 3'ss of exon 5
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgct-gtttgtttaaactttactttttgaactatctttctta---cagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
 ||       |  |  |     |  ||  | |            ||    |||  |  |  |   || |||  | |   |    |  ||| ||| |      ||||| |||||||||||||| ||||| |||||||| ||||| ||||||||||| |||||| |||| || || | ||||||||| ||||||||||| ||||||
-taagatgtgtttttgattgccatcaacggaacttgtctctacctggaaacttcatgtcaagaacgtataagatgt---taacaagttatttttgtatggttagGGAACATGCACCATCAATCATCTTCATGGATGAAATTGATAGTATTGGATCAGCTCGTGTGGAGTCTGGGAATGGCAATGGAGATAGTGAAGTTCAGCGG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 4
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
                                        ||  |  | ||  | || || |     || | ||   |||||   || | |||  |  || |||||||| ||||| || ||||||||||| ||||||||||| ||||| ||  | |||||||| || || | |||||| || || |||||||| ||| | 
--------------------------------------gtatcgtaatgtccatatt-ctatcctagtatagttacgttttt---ctgtgttttct-tagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ28638 (Selaginella moellendorffii), 3'ss of exon 5
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
                                        ||  |  | ||  | || || |     || | ||   |||||   || | |||  |  || |||||||| ||||| || ||||||||||| ||||||||||| ||||| ||  | |||||||| || || | |||||| || || |||||||| ||| | 
--------------------------------------gtatcgtaatatccatatt-ctatcctagtatagttacgttttt---ctgtgttttct-tagAGAGCATGCTCCATCCATTATCTTTATGGACGAGATTGACAGCATTGGCTCGTCCCGTATGGAGTCTGGCAATGGCAACGGGGACAGTGAAGTGCAGAGA

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|110393121|gb|EC958077.1|EC958077
EST:     TACATTGGTGAAGGGTCCAGAATGGTTAGAGAACTTTTCGTGATGGCTAG                         GGAGCATGCACCGTCAATAATCTTTATGGGATGA
genomic: TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACCATCAATAATCTTTATGG-ATGA
EST: gi|110698891|gb|EE076909.1|EE076909
EST:     ACATTGGTGGAAG-CTCCAGAATGGTTAGAGAACTTTTCGTGATGGCGAG                         GGAGCATGCACCATCAATAATCTTTATGGATGAGAATGACAGTATTGGATC
genomic: ACATTGGTG-AAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATC
EST: gi|156737153|gb|EV241267.1|EV241267
EST:     TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCGAG                         GGAGCATGCACCCATCA-TAATCTTTATGGATGAGATTGACAGTATTGGAT
genomic: TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACC-ATCAATAATCTTTATGGATGAGATTGACAGTATTGGAT
EST: gi|26256905|gb|CA807968.1|CA807968
EST:     TACATTGGTGAAGGGTCCAGAATGGTTAGAGAACTTTTCGTGATGGCTAG                         GGAGCATGCACCGTCAATAATCTTTATGGATGAGATTGACAGTATTGGATC
genomic: TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATC
EST: gi|110699382|gb|EE076332.1|EE076332
EST:     TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCGAG                         GGAGCATGCACCCATCA-TAATCTTTATGGATGAGATTGACAGTATTGGAT
genomic: TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACC-ATCAATAATCTTTATGGATGAGATTGACAGTATTGGAT
EST: gi|110733070|gb|EE108911.1|EE108911
EST:     TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCGAG                         GGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATC
genomic: TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATC
EST: gi|30322287|gb|CD005549.1|CD005549
EST:     TACATTGGTGAAGGGTCCAGAATGGTTAGAGAACTTTTCGTGATGGCTAG                         GGAGCATGCACCGTCAATAATCTTTATGGATGAGATTGACAGTATTGGATC
genomic: TACATTGGTGAAGGCTCCAGAATGGTTAGAGAACTTTTCGTGATGGCAAGgtttgtataa ... tttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG
                                        ctatctttctt  CT-rich tract
                tttgtttaaactttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagagcccatcatcaacaataacaaaaaggaaaaaaaaaatgttgctttctttgttgctgtttgtttaaactttactttttgaactatctttcttacagGGAGCATGCACCATCAATAATCTTTATGGATGAGATTGACAGTATTGGATCTGCTCGTATGGAATCAGGAAGTGGCAATGGTGATAGTGAAGTCCAGCGG

- - - cccatca
- - - - - - -tcaacaa
- - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg