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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAATGCTCGTCCATTGCCGCGCCGTCGCTCGCGGCGCCAAGAGGCCGCTTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatgaattctgcacatgaaactgaagctattgttcttcataggttttttttttttccattttttgggtgatcatggtgtttaaatttaatggata...

Basic information

species Vitis vinifera
transcript Vv15s0046g02170.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g12560.1 (Oryza sativa), 5'ss of exon 1
AGAAATGCTCGTCCATTGCCGCGCCGTCGCTCGCGGCGCCAAGAGGCCGCTTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatgaattctgca-----catgaaactgaagctattgttcttcatag--gttttttttttttccattttttgggtgatcatggtgtttaaatttaatggata
 |  |||||||  || |||||||||||||| ||||||||||  |||||||| |||||||| || || || || ||    ||||||||    || |  | ||||     |  |    ||     ||    |  || |||||    |  | | |  | ||  |||| |||||  | | |  |  | ||  || |  |  ||| |     
CGTCATGCTCGAGCACTGCCGCGCCGTCGCCCGCGGCGCCACCAGGCCGCTCCTCGTCGGCGACCTCCCCTTCGGTTGCTATGAGTCCTCCTCCACGCGGgtacacgcgcctctctcatcattcaccccatcgatgctatgccgccgcgttgccgattgattttgttccacatct-gaattttgatc-tgatagacgttatt-----

upper sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA07G06950.2 (Glycine max), 5'ss of exon 3
AGAAATGCTCGTCCATTGCCGCGCCGTCGCTCGCGGCGCCAAGAGGCCGCTTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatgaattctgcacatgaaactgaagct--attgttcttcataggttttttttttttccattttttgggtgatcatggtgtttaaatttaatggata
 || ||||||||||| ||||||||||| || || || ||||||| |||||||||||| || ||  |  | |||||||| || ||||| || || ||||||||  || |      |     |  |      | |  || ||| || ||   | |||   |   |   | |    |   || | |     |||   |||| |  
GGAGATGCTCGTCCACTGCCGCGCCGTGGCGCGTGGAGCCAAGACGCCGCTTCTCGTTGGGGACTTGGCTTTTGGGACCTACGAGTCCAGCTCCAATCAGgtcatgctcgtgcgtattgtttcactcattgttgaatggtttttaatgcttgtttgaataaacttatctggaagcactcgtagaaaagaaaaaaaatgaa--
















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|71864145|gb|DT013200.1|DT013200
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|161721157|gb|FC070393.1|FC070393
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|110685873|gb|EE062975.1|EE062975
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|110685865|gb|EE062960.1|EE062960
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|110684865|gb|EE062628.1|EE062628
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|110732392|gb|EE107638.1|EE107638
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|37190616|gb|CF609965.1|CF609965
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|110685210|gb|EE063373.1|EE063373
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|110711460|gb|EE087965.1|EE087965
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|37185300|gb|CF604653.1|CF604653
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGAT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGAT
EST: gi|71875196|gb|DT024251.1|DT024251
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
EST: gi|37185305|gb|CF604658.1|CF604658
EST:     TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAG                         GCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT
genomic: TTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatga ... ttatgagcagGCAGTTGATGCAGCTGTCAGGATCTTGAAGGAAGGCACAATGGATGCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAATGCTCGTCCATTGCCGCGCCGTCGCTCGCGGCGCCAAGAGGCCGCTTCTCGTCGGTGATCTTCCATTTGGGACATATGAGTCTAGTTCAAATCAGgtattgatgaattctgcacatgaaactgaagctattgttcttcataggttttttttttttccattttttgggtgatcatggtgtttaaatttaatggata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaaa