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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag

Basic information

species Vitis vinifera
transcript Vv08s0007g02170.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 3
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag
 ||    ||||  || || |||||  ||||||| || |||||||| |||||   ||| || ||||||||||| || || |||||||||||||||||||||||||||| ||        ||| | ||   |||    |  | ||   ||   || |   |  | |  |   | | |    || | | |              
GACTTCTGGAGTAAAAGAGGATCGCATGATGATAACCGGAATGCATACTGTGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttgt------gattattttatgttgtcatatatgttgtatt---gcgtagcatctaagttttatggtgcccctactctag--------------

upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G856436_T02 (Zea mays), 5'ss of exon 3
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag
 ||    ||||  || ||||||||  |||||||||| |||||||| ||||||  ||| || ||||||||||| ||||| ||||| |||||||||||||||||||||| ||   | |  |||  || |  ||  | |  | ||   | |||   || |   || ||   | |      | ||                    
GACTTCTGGAGTAAAAGAAGATCGCATGATGATGACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATCGTTGGATGGAAATATgtaagatttgcaacggttatttcgtagtgttcttcgtatatt--gccttgcatctatgtttttatgatgctctt--ctctag-------------------

upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 3
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag
 ||    ||||  || ||||| ||  ||||||| || |||||||| ||||||  ||| || ||||||||||| ||||| ||||| ||||| |||||||||||||||| ||   |  |  || | |   | ||  |   | | ||      |||||   || | |  |  | ||    | |  | | |              
GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg---cgaaggttgtttcatagtgtctccttgtatat-----tgccttgcacctaactttttatgacgctcttctctag--------------

upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G18040.1 (Glycine max), 5'ss of exon 2
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaa--ttctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaatttt--gattatcgaaattag-----------
||| || || ||||| ||||| ||| ||||||| || ||| |||||||||| |||||||||||||||||||  ||||| ||||||||||| |||| |||||||||  |  |||   |||  |  ||||       ||   | ||||  | |      || | | |   | |   |  |||||  || |   | |||   | ||             
CACTGTTGGTGAGAAAGAAGAACGGATGATGATCACCGGATTGCACACTGTCGTTGACATATTCTGTGTTGTATGTGGGTCCATTGTTGGGTGGAGATATgtaaggaccagtttctaaagctcatgttttgcgatttatctgtttacttatcaaaacgtcattggcattgg---gaaatttttgttcttaaaatatttcactttatttcattttag

upper sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G42900.1 (Glycine max), 5'ss of exon 3
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaa-at---tctgttgca--ttgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag------
|||  | || ||||| ||||| ||| ||||| |  | ||| || | ||||| |||||||||||||| ||||  ||||| |||||| ||||||||| |||||||||  || |||   || ||   | | ||||   ||  |||  |  ||| |    |||   |  | |       |||  | | | ||  ||  |||      ||        
CACTTTTGGCGAGAAAGAAGAACGGATGATGCTCTCCGGATTGAAAACTGTCGTTGACATATTCTGCGTTGCATGTGGGTCCATTCTTGGATGGAGATATgtaaggactagtttgtaacatgcatgttttgcgatttatttgtctacttatcaaaatgcaattggcattgggagatttttgttctcaaaattttttactttgttttattttag

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|51052139|gb|CO819409.1|CO819409
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|110702227|gb|EE080703.1|EE080703
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|110390503|gb|EC955415.1|EC955415
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|77580160|gb|DV218980.1|DV218980
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|110424401|gb|EC990761.1|EC990761
EST:     TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|110371533|gb|EC935633.1|EC935633
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|110391310|gb|EC956275.1|EC956275
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
EST: gi|110388162|gb|EC952881.1|EC952881
EST:     TTGTTGACATATTCTGCGTTGGGTGTGGCTCCATTGTTGGATGGAAATAT                         GAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT
genomic: TTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctg ... tcgaaattagGAGGCTGCACATGAGAAGTCCCAACAATACAAGGAAGGAAAATTTATTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA