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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATAACCTGCTCATGGACCGCAAGACCATGGCGCTCAAGATCGCCGACCTCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcctacatcctactactagcagtctctaatctgcttggtgatctgtttcgcatgcgtgatttctgttcttggatctcactgtgatgaatggattatttttcgcag

Basic information

species Oryza sativa
transcript LOC_Os08g40170.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40170.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G068193_T02 (Zea mays), 5'ss of exon 2
GCATAACCTGCTCATGGACCGCAAGACCATGGCGCTCAAGATCGCCGACCTCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcctacatcctactactagcagtctctaatctgcttggtgatctgtttcgcatgcgtgatttctgttcttggatctcactgtgatgaatggattatttttcgcag
||| ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||| |  |||| |||||  | ||||||||||||||||||||| | ||||  || ||    ||      ||  |  |||       ||| |  ||  | ||     || |||                                        
GCACAACCTCCTCATGGACCGCAAGACCATGGCGCTCAAGATCGCCGACCTCGGCCTCAGCCGCGCCATCACCGTCCCGGTGAAGAAGTACACCCACGAGgtcggtttccatcagcc--gcacggatgatccttgttcttggatccgat-taattaacctgaaacgttgctgcag-------------------------------------
















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|29663133|gb|CB659408.1|CB659408
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|29663132|gb|CB659407.1|CB659407
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58604123|gb|CK014651.1|CK014651
EST:     GGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: GGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58676453|gb|CK065140.1|CK065140
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58677365|gb|CK066052.1|CK066052
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|86496840|gb|CI139473.1|CI139473
EST:     ACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: ACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|86593618|gb|CI264497.1|CI264497
EST:     AAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: AAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|58603848|gb|CK014376.1|CK014376
EST:     CAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: CAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|3768776|gb|AU032803.1|AU032803
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTNTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
EST: gi|38479047|gb|CF963180.1|CF963180
EST:     TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAG                         ATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC
genomic: TCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcc ... tttttcgcagATCCTGACGCTGTGGTACAGGGCTCCCGAGGTTCTTCTTGGCGCGGCACAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATAACCTGCTCATGGACCGCAAGACCATGGCGCTCAAGATCGCCGACCTCGGGCTCAGCCGCTCGTTCACTGTCCCTCTCAAGAAGTACACCCACGAGgtccggttcctacatcctactactagcagtctctaatctgcttggtgatctgtttcgcatgcgtgatttctgttcttggatctcactgtgatgaatggattatttttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT