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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaaggattcagcttatggacttcatgtcagtgctctgtaaaatattatttttaatgcatgtggaactagacagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG

Basic information

species Vitis vinifera
transcript Vv07s0031g01480.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G31690.1 (Glycine max), 3'ss of exon 8
-tccaaggattcagcttatggacttcatgtcagtgctctgtaaaatattatttttaatgc--atgtggaactagacagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG
     | | ||||  || |  |   |||     | ||   | |  || ||||  |  | |  || ||  | |       ||||||    |||||| |   ||||||| ||||||||||| ||||||||||| || || ||||||||||| ||||||||||||| |||||||||  ||||||||
tattgatgcttcattttgttcaaggcatactgattcttcatcagttagtattaatgttcctaatatgagagttttttattgactg---ctattctttctgcagATTTCTATCAGCCATTTAAGGAAGATGAACTTGAACAGAGTACTGAAGTTCAAATAATATATCCAGCTGAGCCAAAGCCG

upper sequence: Vv07s0031g01480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G14940.1 (Glycine max), 3'ss of exon 8
--tccaaggattcagcttatggacttcatgtcagtgctctgtaaaatattatttttaatgcatgtggaactagacagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG
        | ||||  || |  |   |||     | ||   | |  || | ||| |  | |  ||   | |||     |      |  |||||| |   ||||||| |||||||| || ||||||||||| || || ||||| ||||| |||||||| |||| |||||||||  ||||||||
ttattggtgcttcattttgtcaagg-cataatgattcttcattagttagtgtttattttcctagtatga-tagttttttagtgactgctattctttctgcagATTTCTATCAGCCGTTTAAGGAAGATGAACTTGAACAGAGCACTGAAGTTCAAATTATATATCCAGCTGAGCCAAAGCCG

upper sequence: Vv07s0031g01480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G14940.2 (Glycine max), 3'ss of exon 8
--tccaaggattcagcttatggacttcatgtcagtgctctgtaaaatattatttttaatgcatgtggaactagacagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG--------------------
        | ||||  || |  |   |||     | ||   | |  || | ||| |  | |  ||   | |||     |      |  |||||| |   ||||||| |||||||| || ||||||||||| || || ||||| ||||| |||||||| |||| |||||||||  ||||||||                    
ttattggtgcttcattttgtcaagg-cataatgattcttcattagttagtgtttattttcctagtatga-tagttttttagtgactgctattctttctgcagATTTCTATCAGCCGTTTAAGGAAGATGAACTTGAACAGAGCACTGAAGTTCAAATTATATATCCAGCTGAGCCAAAGCCGGTAATTACATTGATAGAAAT

upper sequence: Vv07s0031g01480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G39790.1 (Glycine max), 3'ss of exon 8
---------------------------------------tccaaggattcagcttatggacttcat-gtcagtgctctg----taaaatattat-ttttaatgcatgtgg---aactag--acagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG
                                       |  ||    |  |    || |    || || ||||    |    || || ||||| |||| |||  | ||       | |  | | |       | ||||| |  ||||||| || || || || || ||||||||||| || || ||||| ||||| |||||||||||||||||||| ||  ||||||||
gtgagtttctagctctagaatataatttgtctgaatatgtataatagctgtgtacttgtatacaatagttagtggagaggagatataacattatatttttatggttatgatttgctttgttatatcctttaattgttatttttgtaacagACTTCTACCATCCGTTTAAGGAAGATGAACTTGAACAGAGCACTGAAGTTCAAATAATATTTCCAGCAGAGCCAAAGCCG

upper sequence: Vv07s0031g01480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G10010.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------tccaaggattcagcttatggac---ttcatgtcagtgctctgtaaaatattatttttaatgcatgtggaactaga--cagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG
                                                        |   ||    |||  | |   |   |  || |  ||    | ||   | |||| | |   | |||  | |  | |  |   |  ||  | || || | ||  ||||||| ||||| || || ||||||||||| || || |||||||||||||| |||||||| || ||  ||||| |   |   
gtgagttttattcatctactaccaatactagttaaatttgcagagtgaaccatttatagcagatggcaggctgttagcagttgtatattcgtatgttttatcttgttatgtatgtggtatgcagcaacaaattctaatctctcttttttttttctttgcagATTTCTATCAACCCTTTAAGGAAGATGAACTTGAACAGAGTACTGAGGTCCAAATAATGTTCCCCTCTGAACCCCCG---

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|110715682|gb|EE094011.1|EE094011
EST:     AAACACTTGAAGATAGACCGTGTNCA-GAAGTATGAATACTGCCTACCAT                         ATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAAAGTACTGAGGTTC
genomic: AAACACTTGAAGATAGACCGTGT-CAAGAAGTATGAATACTGCCTACCATgtgagttctc ... ctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTC
EST: gi|77585124|gb|DV221654.1|DV221654
EST:     GAAACACTTGAAGATAGACCGTGTCAAGAAGTATGAATACTGCCTACCAT                         ATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTC
genomic: GAAACACTTGAAGATAGACCGTGTCAAGAAGTATGAATACTGCCTACCATgtgagttctc ... ctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTC
EST: gi|22014631|gb|BQ799665.1|BQ799665
EST:     AGAAGTATGAATACTGCCTACCAT                         A-TTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTC
genomic: AGAAGTATGAATACTGCCTACCATgtgagttctc ... ctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTC
EST: gi|351021609|gb|FQ430496.1|FQ430496
EST:     GAAACACTTGAAGATAGACCGTGTCAAGAAGTATGAATACTGCCTACCAT                         ATTTTTATCAG
genomic: GAAACACTTGAAGATAGACCGTGTCAAGAAGTATGAATACTGCCTACCATgtgagttctc ... ctgttaacagATTTTTATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttttaatgcatgtggaactagacagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG
                            agctgac  putative branch site (score: 3)
                                      tcttattct  putative PPT
     ttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaaggattcagcttatggacttcatgtcagtgctctgtaaaatattatttttaatgcatgtggaactagacagctgactggtcttattctgttaacagATTTTTATCAGCCATTCAAGGAAGATGAGCTGGAGCAGAGTACTGAGGTTCAAATAATATTTCCAGCTGAATCAAAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
-ccaagga
- - - - - - gcttatg
- - - - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - - - - - - -taaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgg