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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatgaggtgaacaataatatcttaattaggcattactctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG

Basic information

species Vitis vinifera
transcript Vv04s0008g01040.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 5
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatg---aggtgaacaataatatcttaattaggcatt-actctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG
                          ||   | | | ||| |      | ||     |    |    |||||| |  |  ||| |    ||| |  || ||||||||||||| || |||||||| || ||||| |||| ||||||||||||||||||||| ||||| |||||||||||||| |||||  |||| ||| ||||||
-------------------------gtaacatagtatttttactgtgtagtacaaagtctttaatataacaatcaagtgctaactcaatattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGCTTCATTAAGCCTTGTGCACGGGATATAG

upper sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 5
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgaga-gaatattggatgaggtga-acaataatatcttaattaggcattactctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG
                   | |||| |   || |  | ||  |   |  |||  | | |    | | | ||| || |  ||| |  | || |  || ||||||||||||| || ||||||||||| ||||| |||| |||||| |||||||||||||| |||||  ||||||||||||| ||||  ||||||||| ||||| 
-----------------gtaacctgat---gttgttacttagtagtataaatccttgctatactaatataatcatgtgctaactcagaatcatcctccacagGTTGGTCTACTCAATGTTGATGGTTACTATAACTCTTTGCTCGCATTATTTGACAATGGTGTTGAAGAAGGCTTCATTAAGCATGGTGCTCGGAATATAC

upper sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 5
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatg---aggtgaacaataatatcttaattaggcatt-actctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG
                          ||   | | | ||| |      | ||    ||    |    |||||| |  |  ||| |    ||| |  || ||||||||||||| || |||||||| || ||||| |||| ||||||||||||||||||||| ||||| |||||||| ||||| |||||  |||| ||| ||||||
-------------------------gtaacatagtatttttactctgtagtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG

upper sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 6
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatgaggtgaacaataatatcttaattaggcattactctacacagGT-TGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG
                                                                     || ||| ||  ||  |||||| |  |||  ||| | |   |||  ||   |   ||| ||   | | ||    | ||    || || |    | |||||||    | || |||   |               
-------------------------------------------------------------------gttactattttgctt--gcattatttgacaatggtgttgaagGCTTCATTAAGCGTGGTGCTCGGAATATTCTTGT-CACGGCTTCACCA----GCCAAAGAACTTATGATGAAGATGGAG-------------

upper sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 5
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatgaggtgaacaataatatc--ttaattaggcattactctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG
                    |  | |||   |  |  || | | ||  ||    | |||     ||      | |   ||| || || |||  |      ||||||||||  | ||||||||||||||||| |||  ||||||||| |||||||| | ||||||| ||||||| || |||||||||||||| ||  | || |
-------------------gtatttttaacatttcctttgc-tcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttc-tgtagGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG

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|22014225|gb|BQ799259.1|BQ799259
EST:     AGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCA                         GTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTT
genomic: AGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCAgtaatccgtc ... ctctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTT
EST: gi|110424568|gb|EC990932.1|EC990932
EST:     AGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCA                         GTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTT
genomic: AGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCAgtaatccgtc ... ctctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTT
EST: gi|110396809|gb|EC962509.1|EC962509
EST:     AGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCA                         GTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTT
genomic: AGCTGCTGGAGATGATTACATGGTCGCAACTGGGAATTCATAAAAAACCAgtaatccgtc ... ctctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatattggatgaggtgaacaataatatcttaattaggcattactctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG
                             tcttaat  putative branch site (score: 3)
                                          ttactct  putative PPT
                 tgaacaataatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatgaggtgaacaataatatcttaattaggcattactctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - -caaaaat
- - - - - - - - aaaatcc
- - - - - - - - - - - - - - - - - - - - catgaga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcatta