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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGCACATGTCTGGGATATTCGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtctaactgcagttatgggtgggtgggtcggagcaacttgcacccgtaatctacagatgcttacacaaattttggttgattgaag

Basic information

species Oryza sativa
transcript LOC_Os01g39380.1
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.1 (Oryza sativa), 5'ss of exon 28
lower sequence: GRMZM2G074466_T01 (Zea mays), 5'ss of exon 8
GGTGGCACATGTCTGGGATATTCGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta-actgcagttatgggtgggtgggtcggagcaacttgcacccgtaatctacagatgcttacacaaatt-ttggttgattgaag-
   ||||||||||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||||||| |||    |||| ||     |  |||             | ||  | |        ||  || ||| ||||  || || || ||||  
CACGGCACATGTCTGGGATATTCGCTCCAGCAAGCAGATGTTCAAGCTTCAAGGGCATACAAAGTGGATAAGgtaatttcttcgttgcattttcaactctgtg-------------tacattcatgtgt----gactctgacataaatcatttgtcgactgaaag
















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|112786965|gb|EE591782.1|EE591782
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|29628945|gb|CB633956.1|CB633956
EST:     AAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACTATAATAACTGGGAGTGATGATTGGAC
genomic: AAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|29641895|gb|CB646902.1|CB646902
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|29639658|gb|CB644667.1|CB644667
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|66923642|gb|CX110490.1|CX110490
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACTATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|27547319|gb|CA765549.2|CA765549
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|325493716|gb|JG458240.1|JG458240
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC
EST: gi|38476896|gb|CF961029.1|CF961029
EST:     CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAG                         ATCAATGAGGATGACGGGTGAAACTATAATAACTGGGAGTGATGATTGGAC
genomic: CGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtcta ... ttgattgaagATCAATGAGGATGACGGGTGAAACCATAATAACTGGGAGTGATGATTGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGCACATGTCTGGGATATTCGTTCCAGTAAGCAGATGTTCAAGCTCCAAGGGCACACAAAGTGGATAAGgtaatgtctaactgcagttatgggtgggtgggtcggagcaacttgcacccgtaatctacagatgcttacacaaattttggttgattgaag

- - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA