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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGCTGGGCTTATTGTCACATGGGTCAGTGATCCTATGCATGGGAACACAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactttaccaatgaagccaagattttcaaacttccaggatcttgtcaatccatagattggttattttacactttggggattcattgaggtgcttttctctctttcag

Basic information

species Vitis vinifera
transcript Vv00s1217g00010.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1217g00010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os10g41480.1 (Oryza sativa), 5'ss of exon 4
GCAGGCTGGGCTTATTGTCACATGGGTCAGTGATCCTATGCATGGGAACACAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactttaccaatgaagccaagattttcaaacttccaggatcttgtcaatccatagattggttattttacactttggggattcattgaggtgcttttctctctttcag
 || |||||| | |||||||| |||||||||||||| |||||||||||||| ||||  || ||||||||||| |||||| |||| || ||  | || ||||||||||||      |||      ||||| |   |     |  | |||  |||    | |  | |  |    | | |||||  |||     |  |    | |    ||| ||
CCAAGCTGGGTTGATTGTCACTTGGGTCAGTGATCCCATGCATGGGAACACCATCAGCGCACCATGTGGTCTCAAGACAAGATCATTCGACGCGATCAGGgtaagaactgagggcatg---ttcagattgtagtaaaaataa-accttaccaacttttggcattgcca----aaattttggcaatttgacaatat----tgccaagttttag

upper sequence: Vv00s1217g00010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA15G06020.1 (Glycine max), 5'ss of exon 4
GCAG-GCTGGGCTTATTGTCACATGGGTCAGTGATCCTATGCATGGGAACACAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactttaccaatgaagccaagattttcaaacttccaggatcttgtcaatccatagattggttattttacactttggggattcattgaggtgcttttctctctttcag
 ||| || || |  |||||||| ||||| ||||| || |||||||||||||| || || || |||| ||| || || || || ||||||||| | ||||||||||           |    |     |||||   |  | ||  || | | | || || |  | |  |||   | | | |||   || | | ||  | |||||| ||      
-CAGAGCAGGTCAAATTGTCACTTGGGTTAGTGACCCCATGCATGGGAACACCATTAAAGCTCCATCTGGACTTAAAACCCGCTCTTTTGATGCAATAAGGgtaattttcacttatacttggttcctatttt---atattcaatatttaggctatacacaagtggcatat---aaaatctggtc-tttactaagtcgtttttctatcc-----

upper sequence: Vv00s1217g00010.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S76_162V6.1 (Physcomitrella patens), 5'ss of exon 4
GCAGGCTGGGCTTATTGTCACATGGGTCAGTGATCCTATGCATGGGAACACAATCAAGGCCCCATGT---GGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactttaccaatgaagccaagattttca--aacttccaggatct---tgtcaatccatagattggttattttacact---ttggggattcattgaggtgc---ttttctctctttcag--------------------------------
   ||||||    || || || |||||||||||||| ||||| |||||||||||||| || ||  |    ||   |||||| ||| | || ||| | ||   |||||       |||   || | ||  || ||||  || ||||   ||||   |  |||  |  |    |  | |     |     ||        ||       |   | |||| ||  | ||                                
---GGCTGGATGCATGGTGACCTGGGTCAGTGATCCCATGCACGGGAACACAATCAAAGCACCTGGCTCCGGAACGAAGACGCGACCCTTCGATGCCATTCTGgtaattgtcgaaccttcgaggacacaatcttcatgaatttcctccatctagatagcaaatctcatccagcctgtcccgaaaccaattaacaccatatcctaacaccagtgttctatcactgaggacgctgtggctggtgtctgggcccaatgcag

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|27583676|gb|CB006371.1|CB006371
EST:     CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGG                         TCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
genomic: CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactt ... tctctttcagTCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
EST: gi|27585432|gb|CB008127.1|CB008127
EST:     CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGG                         TCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
genomic: CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactt ... tctctttcagTCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
EST: gi|27581844|gb|CB004539.1|CB004539
EST:     CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGG                         TCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
genomic: CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactt ... tctctttcagTCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
EST: gi|110699625|gb|EE076785.1|EE076785
EST:     CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGG                         TCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
genomic: CAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactt ... tctctttcagTCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
EST: gi|110408359|gb|EC973994.1|EC973994
EST:     CTGAAGACACGATCTTTTGATTCTATAAGG                         TCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA
genomic: CTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactt ... tctctttcagTCAGAATTGCGAGCTTTCTTTGATGTTCATGATCAAGAAGGGAGCCACCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGCTGGGCTTATTGTCACATGGGTCAGTGATCCTATGCATGGGAACACAATCAAGGCCCCATGTGGTCTGAAGACACGATCTTTTGATTCTATAAGGgtaagaactttaccaatgaagccaagattttcaaacttccaggatcttgtcaatccatagattggttattttacactttggggattcattgaggtgcttttctctctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA