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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcacggaaattaggatttgtctttttttgggacggagggagtatgtacatttcagacataccatggctcattgtcagtgacccctcgattccggtgcagGTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTCAACGAAGGGAGGGATGTGATCATGGACGGCACCATGTCGTGGGAGCCGT

Basic information

species Oryza sativa
transcript LOC_Os05g43300.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43300.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G368410_T01 (Zea mays), 3'ss of exon 5
ggcacggaaattaggatttgtctttttttgggacggagggagtatgtacat-ttcagacataccatggctcattgtcagtgac--ccctcgattccggtgcagGTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTCAACGAAGGGAGGGATGTGATCATGGACGGCACCATGTCGTGGGAGCCGT
         ||||  ||    | |  | | | ||      |   || | || || |        |    |     ||| ||||  ||| | ||  || ||||||| || ||||||||  |||||||||||||||||||||| || ||||| |||||||||||  |||| ||||||||||| |||||  |||| ||||||||||
---ttccgcattaacatgcaccatgatctcgcacctttacatattgcagatgtttacggcctttaaaattagacttcaatgacgacccgccatcacgatgcagGTGCACCAGTCATCCTTGGACGCAGCCTCGTCGCTCCTCGTCACTGCACTCAACGAAGGCCGGGACGTGATCATGGATGGCACTCTGTCCTGGGAGCCGT
















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|218505355|gb|FG968511.1|FG968511
EST:     CTATCAGCTCAAGAGGCCACCACAATGACATGCTGCAGACGGCAGAACTG                         GTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTC
genomic: CTATCAGCTCAAGAGGCCACCACAATGACATGCTGCAGACGGCAGAACTGgtatttgtta ... tccggtgcagGTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTC
EST: gi|88353182|gb|CI654448.1|CI654448
EST:     ATGCTGCAGACGGCAGAACTG                         GTACATCAGTCATCGATGGACGCAGCGTCGTCGCTCCTGGTGACTGCCCTC
genomic: ATGCTGCAGACGGCAGAACTGgtatttgtta ... tccggtgcagGTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTC
EST: gi|88344019|gb|CI638754.1|CI638754
EST:     ATGCTGCAGACGGCAGAACTG                         GTACATCAGTCATCGATGGACGCAGCGTCGTCGCTCCTGGTGACTGCCCTC
genomic: ATGCTGCAGACGGCAGAACTGgtatttgtta ... tccggtgcagGTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcacggaaattaggatttgtctttttttgggacggagggagtatgtacatttcagacataccatggctcattgtcagtgacccctcgattccggtgcagGTACATCAGTCATCGATGGACGCAGCCTCGTCGCTCCTGGTGACTGCCCTCAACGAAGGGAGGGATGTGATCATGGACGGCACCATGTCGTGGGAGCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatggc