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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagatatatgcatcagatagagcctcctgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa...

Basic information

species Vitis vinifera
transcript Vv08s0007g03610.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 5'ss of exon 9
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagatatatgcatcagatagagcctcctgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa--
 || ||||| |||||||| |||||||||||||||||||| || ||||| || || ||  | || ||||| || || |  |||||||||||||||||||||||||||     | |  | | |   |     ||        | ||| | || ||  |||        |  |||  || |    |     | | || |||||  
CAGTGTGCTTGAAGCTGATATTGTTGTTGTTGGTGTTGGGGGCAGACCGCTGACTACTCTCTTTAAAGGTCAAGTTGCTGAGGAGAAAGGTGGAATTAAGgttagtttgctttta-acctgtaggcttgaccacagaaggtgctagggatgtttctatcaaagaaacagtgtgtaaacaac-tggacgtttctttatcaaaa

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 8
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagt---agatatatgcatcagatagagcctcctgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaat-atattgatcaa--------------------------------------------------------------------------------
 |  ||||||||||||||||||||| |||| ||||| ||||| || || || ||     | ||||| || || || | ||||||||| |||||||| |||||| ||      | | | ||||    |||  || || | | |  |  |  | ||   | ||   |   | |  |   | | || |||| | | |   | || |                                                                                 
AAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAGTTGCAGAGGAGAAGGGTGGAATCAAGgtttgtccggtttctgttcatctttcagattctgctctatctgctacatttgttgcgtgatgattgtatttcaggctattgtccatttgagtcaccctaattagcaactgaaccttctttcgagcttgttcttgcttataccttcgaattagctgaacatttcaaatctgcatgtgtcttccag

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 8
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtaga--tatatgc-atcagatagag-cctcctgtttttcttctaagtatt-ttattattggtccttctttgtagaatctctattttaatat-attgat-caa----------------
 ||||| ||||||||||| |||||||| ||||||||||| ||||| || |  ||| | ||| ||||||| ||||| ||||||||||| |||||||| ||||| |||      |||| | || |    ||| | |  |      ||   || | || ||||     |||     | || || |||     | ||| | | |||| | |                
CAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatccgattatccggaggcttgttaacaggctataaaatgttgttatcccaagtcgggaatagt-gattcttgtcatcaatgtcaatgatgccatttgttttggttgcag

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 8
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtag----atatatgca---tcagatagagcctcc----tgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa------
 ||||| ||||||||||| |||||||||||||||||||| ||||| || |  |||   ||| ||||||| ||||| ||||||||||| |||||||| ||||| |||      |||| || |   |     | || ||      |||| |  | |  |||| |  || | || | ||| ||  |  ||| || ||  |   || |   |         
CAGGGTCCTGGAAGCTGATATTGTTGTTGTTGGTGTTGGAGGAAGGCCTCAAACAGTCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatctggaggcttgttgacaggctataaaatgttgtcatccggagtagtgaat-agtgattcttgtt-atcaaatatcaatgatgccatttgttttggttgcag

upper sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 8
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagatatatgcatcagatagagcctcctgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa
 |||    ||||||| ||||||||  | ||||| ||||||| || |||  | ||| | |||||||| |||||||| || || || |||||||||||||||||    |  ||| |||  |   | | | ||| | || ||||| |     |   ||| |   |      || || | |  ||  || | | | |    || 
GAGGACATTGGAAGCCGACATTGTGATAGTTGGGGTTGGTGCAAAACCATTGACATCCTTATTCAAGGGACAGGTCGAGGAAGATAAAGGTGGAATTAAGgt----atttatctgctgcctgt-gcgtctcttcttcttcttatcc-cgtaccattctgatttggatcttttaaattgactgcttaactgtttcacacag

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|110723311|gb|EE100477.1|EE100477
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAA-CAAGTGTTCCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
EST: gi|161709350|gb|FC059679.1|FC059679
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAAACAAGTGTACCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
EST: gi|110373500|gb|EC937742.1|EC937742
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
EST: gi|161713126|gb|FC062484.1|FC062484
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
EST: gi|33403613|gb|CF209240.1|CF209240
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
EST: gi|29784398|gb|CB345068.2|CB345068
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
EST: gi|26264446|gb|CA815509.1|CA815509
EST:     TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAG                         ACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT
genomic: TTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagat ... ttgactgcagACTGATGAATTCTTCAAAACAAGTGTTCCTGATGTATATGCTGTGGGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtagatatatgcatcagatagagcctcctgtttttcttctaagtattttattattggtccttctttgtagaatctctattttaatatattgatcaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agatagag