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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCTGTACCAGCTCCTCTTGGTGGTGTCATAATTATTGGTGAGGAGACAATAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatattgttctctttatggttcttagatttgtggtgcctactgtgtgtgcaggtatgttggcactccataactaattgtttttgtcttccattcttgtacag

Basic information

species Oryza sativa
transcript LOC_Os05g51480.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51480.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 9
ACCTGTACCAGCTCCTCTTGGTGGTGTCATAATTATTGGTGAGGAGACAATAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatattgttctctttatggttcttagatttgtggtgcctactgtgtgt--gcaggtatgttggc-actccataactaat-tgtttttgtcttccattcttgtacag----------
||| ||||||||||| ||||| ||||| ||||| ||||| |||||   ||||||||||||||||||||| || ||||||| ||| |||||||| ||||| ||||| | |||    | |     |  ||   ||||||||||| |||   |||  |  ||||   |||| || | |   ||||  |  || | |  ||| |  ||    |           
ACCAGTACCAGCTCCACTTGGCGGTGTGATAATAATTGGCGAGGAACAAATAGTTTACTGCAATGCCAATTCCACATTTAAAGCGATACCAATAAAACAAgtaatctcttgcctacatctctttatttttctttgtggtgccaacttcatgttggttggtaccgtggctacactaattctaacataattcttttctccttgattactgatttcttggcag
















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|86904800|gb|CI310593.1|CI310593
EST:     TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCTATCAAACAG                         TCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
genomic: TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatatt ... tcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
EST: gi|29669278|gb|CB665553.1|CB665553
EST:     TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAG                         TCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
genomic: TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatatt ... tcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
EST: gi|86894503|gb|CI308252.1|CI308252
EST:     TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAG                         TCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA
genomic: TAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatatt ... tcttgtacagTCAATCATAAGAGCTTACGGACGGGTTGACCCAGACGGTTCGCGCTATTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCTGTACCAGCTCCTCTTGGTGGTGTCATAATTATTGGTGAGGAGACAATAGTTTACTGCAATGCCAACTCTACATTTAGAGCTATACCAATCAAACAGgtaatatattgttctctttatggttcttagatttgtggtgcctactgtgtgtgcaggtatgttggcactccataactaattgtttttgtcttccattcttgtacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT