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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaagtagggaaaaaaggtgatgctttggtaggagggagtatcatctgccaatgacattgttcaactaaaaattttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA

Basic information

species Vitis vinifera
transcript Vv19s0090g00560.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 11
-------------------aattaagtagggaaaaaaggtgatgctttggtaggagggagtatcatctg--ccaatgacattg----ttcaactaaaa-attttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA
                     ||   |     |         |   ||  ||    | | || || | |  | ||  || |      || |||  |   |  ||    || |    |  | | ||||||| ||||||||||||||||| || |||| ||| |  || ||||| |||||||| |||||||| || ||||  ||    | ||||||| ||||||| ||
gtaagctccctacctcctatcttgcatttattatctgaagcttctcttcatacctagcaataccaaccggacgaacaacgtaaacatttgaaccgagtcacattttcgtgtcg---tcgatcacagATTGCGAGTGGAAAGCTCAGGCGGGGAACACCTGCGCCGCGTCATTCGACTGGAGATGCAGCGGCATATGCAACTCGGAGGGGAGGATCTGGGAGGTGCA

upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 10
aattaagtagggaaaaaaggtgatgctttggtaggagggagtatcatctgccaatgacattgttcaactaaaaattttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA
         |  ||||||  | | | |    ||        |||   |    |  ||  || |     |   | || | |       |     || ||||||||||||||||| || ||||| ||||||||||||||||| || || || ||||||||||| |||||||| |||||  | || ||||| | ||| || ||
---------gtaaaaaaaattcaagttcccttatc------tatgtccaagtatggaagttttctcgattccatttgttgatcaatgagaa--actgcagATTGTGAGTGGAAGGCGCAGGCGGGCAACATCTGTGTTGCCTCGTTCGATTGGAGCTGCAGTGGGATTTGTAGATCAGCGGATAGGATGAAGGATGTTCA
















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|34544134|gb|CF512366.1|CF512366
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|349826233|gb|FQ416038.1|FQ416038
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|71875910|gb|DT024965.1|DT024965
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|77583730|gb|DV220900.1|DV220900
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|34544220|gb|CF512452.1|CF512452
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|71875911|gb|DT024966.1|DT024966
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|110385919|gb|EC950479.1|EC950479
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|351046999|gb|FQ454609.1|FQ454609
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|110712361|gb|EE089898.1|EE089898
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
EST: gi|351056608|gb|FQ442436.1|FQ442436
EST:     GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAG                         ATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT
genomic: GGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGTACCCCACCAGgtaatgttat ... tttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgccaatgacattgttcaactaaaaattttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA
                    aactaaa  putative branch site (score: 2)
                                           tttttacc  putative PPT
                 ttcaactaaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaagtagggaaaaaaggtgatgctttggtaggagggagtatcatctgccaatgacattgttcaactaaaaattttgggatgccaatttttaccgcagATTGTGAGTGGAAAGCTCAGGCAGGCAACATCTGTGTTGCTTCATTTGACTGGAGCTGCAGCGGGATTTGCAGATCTTCTGAGAGGATCAGGGAGGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - -gaaaaaa
- - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - tctgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgcc