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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag

Basic information

species Vitis vinifera
transcript Vv16s0050g00800.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00800.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os11g37130.1 (Oryza sativa), 5'ss of exon 2
GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag
 |  |  |||||||| ||| | ||||| ||||| ||||| || |||||||| ||||||||||| ||| |||| || |||||||||||||| || || ||||||| || | |    | ||     | ||| | | | ||||| |   |  ||            | | | ||  |   ||    || |  |  |  | |     ||                                                                    
AACGGGTGTTTATGCTTCTTTATTTGGAGTTGGAGCTCCCGAAGCTCTGGTCATTGGAGTGGTTGCTCTGTTAGTCTTTGGTCCCAAAGGACTAGCAGAGgtaaactctttcccaacaa-----acctggacatcatatttttgctgttgtccggcttcctattctagctaattc--ttcactaaaccctcagcattagcaccatat------------------------------------------------------------------

upper sequence: Vv16s0050g00800.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os06g01290.1 (Oryza sativa), 5'ss of exon 2
GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag
 |  |  ||||| || ||| | ||||| ||||| ||||| || |||||||||||||||||||| ||| |||| || ||||||| |||||| || || ||||||| || | |      ||    | ||   | |  ||   ||| ||   |  ||   |   |   |  ||  ||| | ||      ||   |  || |||  ||                                                                     
AACTGGTGTTTACGCTTCTTTATTTGGAGTTGGAGCTCCCGAAGCTCTGGTTATTGGAGTGGTTGCTCTGTTAGTCTTTGGTCTCAAAGGACTAGCAGAGgtaaactctttcccagcaagcctagacatcatatttttgctgt-tgtccggcttcctattctagctaatt--cttcactaaaccctcagcattagt-actccaa---------------------------------------------------------------------

upper sequence: Vv16s0050g00800.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G37690.2 (Glycine max), 5'ss of exon 2
GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag
 || ||||||||||| ||||| ||||||||||| |||||||||||| |||| ||||| || || ||||||||||||||||| || ||||||||||||||||| | ||   |  || |   |  |  |     ||  |   ||| |     |||| |     | |      || |||||| ||   ||||||   |  | | |  || | ||||                                                            
TAAGGTGGTTTATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagcttgattgatgtgtctctatgc----aactattgctgtgtcattctttttg-----tttcaaagaattttaattttttttgcattt---gctattct--tgtttgttgt-----------------------------------------------------------

upper sequence: Vv16s0050g00800.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G30120.1 (Glycine max), 5'ss of exon 2
GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaa--tctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag
 |||||||| ||||| ||||| ||||||||||| |||||||||||| |||| ||||| || || ||||||||||||||||| || ||||||||||||||||| |  |   |  || | ||  |    ||      |  | | |  ||     ||||  || ||| ||   |  | ||   |||      ||| | | |   |||                                                                       
TAAAGTGGTATATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTTTGGCCCTAAAGGTCTTGCTGAGgtgagtttgattgatgtgtatctatgtacctcttgctctgtgt-cattctttttttcaaagaattttaaatgtttttgcatat---gctattcttgtttgttgt-----------------------------------------------------------------------

upper sequence: Vv16s0050g00800.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT5G52440.1 (Arabidopsis thaliana), 5'ss of exon 2
GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaa---tctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag
 |   || ||  ||| ||||||||||| ||||| || ||||||||| |||||||||| || || |||||||| || |||||||| ||||||||||||||||| |   ||| ||| | | |||   |   ||  |    | ||||| |   |  | ||   |    ||||    | ||||   |||    |  ||| | |  || |                                                                       
TATGATGATTCGTGCGTCTCTGTTTGGTGTTGGAGCACCTGAGGCTTTGGTTATTGGTGTTGTTGCTTTGTTAGTCTTTGGTCCTAAAGGTCTTGCTGAGgttagtgtctttgtgtgtgtaa--aatttcttgatgattgatttggaatcatatctttttagg--gtttaagcaacttatgaattagtactgtttagttt-ctct-----------------------------------------------------------------------

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|351024828|gb|FQ430653.1|FQ430653
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|351014666|gb|FQ437866.1|FQ437866
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|351024434|gb|FQ426243.1|FQ426243
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|110375864|gb|EC940884.1|EC940884
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|161709637|gb|FC058421.1|FC058421
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCG
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCG
EST: gi|77581466|gb|DV219665.1|DV219665
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|110387630|gb|EC952313.1|EC952313
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|351026337|gb|FQ428349.1|FQ428349
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|110402322|gb|EC959863.1|EC959863
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|26262405|gb|CA813468.1|CA813468
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAANTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|161716016|gb|FC068769.1|FC068769
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
EST: gi|351025830|gb|FQ427842.1|FQ427842
EST:     TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAG                         GTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA
genomic: TTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtg ... cttaatgcagGTTGCTCGGAATTTGGGAAAGACTTTGCGTGAATTTCAGCCCACAATTAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTTTGGTCCCAAAGGTCTTGCTGAGgtaatctgtgtatatataattgaaaactgaagaccttatttgtatggaagttttagaaaaatgtttggttatcttaattattgaagcattttgggtgactgtaatgctggttgcagagacttagattctgtgttttgccttttagtatctttgtttttattatcttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG