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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaattgactcacttggtaacttaattgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG

Basic information

species Vitis vinifera
transcript Vv05s0102g01180.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 2
cttaattgactcacttggta-acttaattgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttt----tccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
||||  ||  |  |||| |   | |||  |  |   ||||  | || |   || |   |  || |   |  |   |      |||  |||    | | | |  ||||||| || ||  | || |||||||| ||  |  ||||||| || ||||| || |||||||||||||| || |||||||||||    ||  | ||| |||
ctta--tgctttccttgcttcgcataaaagggtta-ttggggatagctacattggaattatctatagtatttg--ttgccaacaatgtttatgcttcttgtgtagGTACCCTGCCTTCAAGATAACTATGCTTACATCCTACATGATGTTGATACTGGAACAGTTGGAGTTGTGGACCCTTCTGAAGCAACGCCAATCATAAATG

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G03320.1 (Glycine max), 3'ss of exon 2
------------------------cttaattg----actcacttggtaacttaattgactcgct--tggtaacagttctttttgtg--cttcctttcacacataaatctttgtcaactttttccg----------tcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
                         | | |||      ||   | | |   ||| |   || |   || | | |  | || |   |   |    |  |  | |||||  |     | | | |             |  | ||||||| || ||||||||||| ||||||||||| |||||||| || ||||| || |||||||| |||||||||||||||||||| || ||||| |||||||
gtgagagcgggtctcttattagttttcagttgctgtggtcctgttggattataaataggtcacccgtgctgataagttttctgaagaaatatgctgaaagcctaaattgtgacttattgtctttaaaaaaaaatattgttagGTACCTTGCCTGAAGGACAATTATGCATATCTGTTACATGATGTAGATACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTGTCATAGATG

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G13470.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------cttaattgactcacttggt-aacttaattgactc--gcttggta-acagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
                                                           ||| |      | ||| | ||  ||||   |||  |     ||  | |   || | |||  | || |   || ||  || || |   ||||||   |  | |||| ||||| || | |||||| ||||||||||||||||| || || ||||| || |||||||| |||||||||||||||||||| | |||| | |||||||
gtgagcagatctcttcttccttttttaaaggtttttttgtgatgcaattagattagtatttagtcactcaagttgctcaagctaataagctctggagcaatatgctgaaattctagtgtgtgctgtgttacttatctcattttt--ctttttgaattgttagGTTCCATGCCTTAGGGACAATTATGCATATCTTTTACACGATGTGGATACGGGGACAGTTGGTGTTGTTGATCCTTCTGAAGCTGCACCTATCATAGATG

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
--------------------------------cttaattgactcacttggtaac--ttaattgactcgc-ttggtaacagttct-------ttttgtg----cttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
                                 || || |    | | | | ||  |||  | || ||   || |||   ||||       | |  ||    |||   |||  || | | | | | | || |||||   |  | ||||||| || ||||||||||| ||||| ||||| |||||||| || || || || |||||||| |||||||||||||||||||| || ||| | |||||||
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaatttttt--ttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G05470.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------ctta--attgactcacttg-gtaacttaa-ttgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctt-tgtcaacttt-ttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
                                                  |||  ||| | |||||   ||  || ||  | |   |||  | | |  |    |     | |    |      |   |||| | |||  ||| ||   |  | |||| |||||||| | |||||| ||||||||||||||||| || || ||||| || |||||||| |||||||||||||| ||||| |  ||| | |||||||
gtgagcagatctcttcttcctttttataaggcttttgtgatgcaattagattagtatttagtcactcaagttgctcaagctaataagctctggagccatatgctgaaatcctagcatgtgctgtgtttcttatctcatttttctttaattgttagGTTCCATGTCTTAGGGACAATTATGCATATCTTTTACACGATGTGGATACGGGGACAGTTGGTGTTGTTGATCCTTCCGAAGCTGCGCCTATCATAGATG

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
cttaattgactcacttggtaactta---attgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
 ||| ||||  |  ||  | |  |    ||| | | |  |  |||   |    |           || |    |   |    |  |||  ||    | ||||||| |||||||| | |||||||||||| ||| | |||||||| |  ||||| || |||||||| || ||||| ||||||||||| ||||||||||| ||||
-ttacttgaaccgtttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttgtttagcagtc--ttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG

upper sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
cttaattgactcacttggtaacttaattgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgt---cttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
     ||      |||   | ||| | |     | |||  ||||  ||| |      |    |  | | || | |     || | |||          ||||||| || ||    |||||||||||||| ||||| || || || |  || || || ||||||||||| |||||||||||||| || | |||||||||||| |
----gttagtatgcttttcatcttgaatctactggttga-aacaactctgta-acaatctgctgaagatattattaacgatctattttactgagatgtttcagGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG

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|110718180|gb|EE094717.1|EE094717
EST:     CGCAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTG                         GTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
genomic: CACAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTGgtgagcatct ... ccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
EST: gi|110715392|gb|EE093393.1|EE093393
EST:     CACAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTG                         GTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
genomic: CACAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTGgtgagcatct ... ccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
EST: gi|34549778|gb|CF518010.1|CF518010
EST:     CGCAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTG                         GTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
genomic: CACAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTGgtgagcatct ... ccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
EST: gi|110688962|gb|EE068114.1|EE068114
EST:     CGCAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTG                         GTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA
genomic: CACAATTTTGCAGTGTTTCCAATACGTCTTCCACATTGCAAATTGAATTGgtgagcatct ... ccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttttgtgcttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG
                                       ctttttccgtcttc  CT-rich tract
                        ataaatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaattgactcacttggtaacttaattgactcgcttggtaacagttctttttgtgcttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - -cacttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acataaa