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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTATAAAGGCCGTGCTCCAAGTAAAGAGCGCACAGACTGGGTGATGCATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgctcaaaatgatttttttttttaattattagtatcttatgtcgataattgtctattgaaattggttatctttccatgtttcag

Basic information

species Vitis vinifera
transcript Vv18s0001g01820.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01820.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G36360.1 (Glycine max), 5'ss of exon 2
TTTCTATAAAGGCCGTGCTCCAAGTAAAGAGCGCACAGACTGGGTGATGCATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgctcaaaatgatttttttttttaa--ttattagtatcttatgtcgataattgtct--at--tgaaattggt--tatctttccatgtttcag-----------------------
||||||| ||| | ||||| ||| ||||| || || ||||| |||||||| ||||| |||||||||||||||| |||||||||| | ||| ||||| ||||||| || || || | | | || | | |||| | | || ||| | || ||| | | ||| |
TTTCTATGCTGGCAGAGCTCCTAGTGGTGAGCGGACTGATTGGGTTATGCATGAATATACCTTGGATGAAGAGGAGCTTAAGAGATGCCTGGGTGTTAAGgtaccacttaattggccattttttgcttcaaatttctcgatttgttgttttcttaatcattttgatcatgagaagagtactatttactgacctttgggttttgatataaatttatcttcag

upper sequence: Vv18s0001g01820.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G31210.1 (Glycine max), 5'ss of exon 2
TTTCTATAAAGGCCGTGCTCCAAGTAAAGAGCGCACAGACTGGGTGATGCATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgctcaaaatg--atttttttttttaattat--tagtatcttatgtcgataattgtct--at--tgaaattggt--tatctttccatgtttcag-----------------------
|||||| |||| | ||||| ||| ||||| || || ||||| |||||||| || || |||||||||||||||| |||||||||| | ||| |||||| || || || ||||||| || |||| | | | | || | | || | | | || ||| | || ||| | | ||| |
TTTCTACGCAGGCAGAGCTCCTAGTGGTGAGCGGACTGATTGGGTTATGCATGAATACACCTTGGATGAAGAGGAGCTTAAGAGATGCCAGGGTGTTAAGgtatc--acttaatttgccattttttgcttcaattttcttgatttgttgttttcttactcattttgatcatgagaagagtactatttactgacctttgggttttgatataaattcatcatcag
















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|161718568|gb|FC065387.1|FC065387
EST:     AATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAG                         GATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTCCCAAA
genomic: AATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgct ... catgtttcagGATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTCCCAAA
EST: gi|161720508|gb|FC070907.1|FC070907
EST:     ATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAG                         GATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTCC-AAA
genomic: ATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgct ... catgtttcagGATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTCCCAAA
EST: gi|161716141|gb|FC068060.1|FC068060
EST:     ATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAG                         GATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTCCCAAA
genomic: ATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgct ... catgtttcagGATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTCCCAAA
EST: gi|161720743|gb|FC070650.1|FC070650
EST:     ATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAG                         GATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTC
genomic: ATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgct ... catgtttcagGATTATTATGCACTTTATAAGGTCTTCAAGAAGAGTGGACCTGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTATAAAGGCCGTGCTCCAAGTAAAGAGCGCACAGACTGGGTGATGCATGAGTATACAATGGATGAAGAGGAGCTCAAGAGATGCCCGAATGTGCAGgtattttgctcaaaatgatttttttttttaattattagtatcttatgtcgataattgtctattgaaattggttatctttccatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG