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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTGGCTTACCACATTGAGAAACCTTGTTGCTCAAATAAATGAGACCTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcattatagttccttcaataaaatttattttttgagaagactgcttgcttattcttttgatttgatgtttctttttttttctcag

Basic information

species Vitis vinifera
transcript Vv13s0064g00180.t01
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0064g00180.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: LOC_Os05g51790.2 (Oryza sativa), 5'ss of exon 23
GAAAATTGGCTTACCACATTGAGAAACCTTGTTGCTCAAATAAATGAGACCTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcattatagttccttcaataaaatttattttttgagaagactgcttgcttattcttttgatttgatgtttctttttttttctcag---------
|  || |||||| | ||  || | |  |||||| |  |||||||    || |||||||| ||||| ||||| |||||||||||||||||||||||| | |||||   |   ||||||||        ||| | || | | |    |  |||  || | |||| |  ||   |  |  | | |  |  |          
GGCAAATGGCTTCCAACTCTGCGCACTCTTGTTTCAAAAATAAACAGCACGTTTAGTCGTAACTTTCAAGAAATGGCTGTTGCTGGAGAAGTTTCACTTGgtatgtgtggcagttccttt-------tttgtgttatcacactgttatttg--tactattttcagatggcataccaatctgtaccaaatttcctgcag

upper sequence: Vv13s0064g00180.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: GRMZM2G440916_T01 (Zea mays), 5'ss of exon 23
GAAAATTGGCTTACCACATTGAGAAACCTTGTTGCTCAAATAAATGAGACCTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcattat--agttccttcaataaaatttattttttgagaagactgcttgcttattcttttgatttgatgtttctttttttttctcag
|  || |||||| | ||  || | |  |||||| |  ||||||| || || || ||||| ||||| ||||| ||||| || ||||||||||||||| |||||||  || ||   ||| ||||   |   ||| |||| |  ||  ||  | |  || |  | |  |    |  ||||||            
GGTAAATGGCTTCCGACTCTGCGGATTCTTGTTTCAAAAATAAACGACACATTCAGTCGTAACTTTCAAGAAATGGCAGTCGCTGGAGAAGTTTCACTGGgtatgtatgattttgtttcttcgccattgtttgttttgtttgataacaccctaattgtcgtgtcaa----acctttcttgcag--------

upper sequence: Vv13s0064g00180.t01 (Vitis vinifera), 5'ss of exon 23
lower sequence: GLYMA20G34020.1 (Glycine max), 5'ss of exon 24
GAAAATTGGCTTACCACATTGAGAAACCTTGTTGCTCAAATAAATGAGACCTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcattatagttccttcaataaaatttattttttgagaagactgcttgcttattcttttgatttga--tgtttctttttttttctcag
| ||| |||||| | ||||||||||||||||| ||  | |||||||| || || |||   || |||||||| |||||||||||||||||||||||| | ||| |     || |       | ||| ||  |  | ||| |        || |||| ||||||    | |  | | | |  | | |||||||
GGAAAATGGCTTCCAACATTGAGAAACCTTGTGGCAAAGATAAATGAAACATTCAGTTTTAATTTCCAAGAGATGGCTGTTGCTGGAGAAGTTTCACTAGgtctgtcagatggca-----attaacatgaacatgttgggt------ttttcttactcttttatcctcacctatgtttcatgtcttctcag

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|351031040|gb|FQ444867.1|FQ444867
EST:     CTTTAGTCGAAACTTCCAAGAGATGGCTGTTGCTGGAGAAGTTTCATTGG                         ATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
genomic: CTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcatta ... tttttctcagATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
EST: gi|351032202|gb|FQ460459.1|FQ460459
EST:     CTTTAGTCGAAACTTCCAAGAGATGGCTGTTGCTGGAGAAGTTTCATTGG                         ATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
genomic: CTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcatta ... tttttctcagATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
EST: gi|351031564|gb|FQ459821.1|FQ459821
EST:     CTTTAGTCGAAACTTCCAAGAGATGGCTGTTGCTGGAGAAGTTTCATTGG                         ATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
genomic: CTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcatta ... tttttctcagATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
EST: gi|351037685|gb|FQ464126.1|FQ464126
EST:     CTTTAGTCGAAACTTCCAAGAGATGGCTGTTGCTGGAGAAGTTTCATTGG                         ATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT
genomic: CTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcatta ... tttttctcagATGAGCATGATATCGATTTTGATCAATTTGGGATACTTATAAAAGTCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAATTGGCTTACCACATTGAGAAACCTTGTTGCTCAAATAAATGAGACCTTTAGTCGAAACTTCCAAGATATGGCTGTTGCTGGAGAAGTTTCATTGGgtattcattatagttccttcaataaaatttattttttgagaagactgcttgcttattcttttgatttgatgtttctttttttttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT