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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgtgttcgcattgtactatgaagaaacaactaatgcatcattgtccttcattagccttaatcgttggagctaaatattctcttttggtgtaaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGATATACTGAACGAATTTTTGCTTACACAAGGGGATGGAGTGTAGAACATCA

Basic information

species Oryza sativa
transcript LOC_Os04g36062.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36062.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G158097_T03 (Zea mays), 3'ss of exon 11
-----ccgtgttcgcattgtactatgaagaaacaactaatgcatcattgtccttcattagccttaatcgttggagctaaatattctcttttggtgtaaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGATATACTGAACGAATTT-TTGCTTACACAAGGGGATGGAGTGTAGAACATCA
       |     ||| | |||||||  | | ||     |||||   | ||   | ||  ||| || | |   | |||| |||   |   || |   |||  |||||||| |||| |||||||||||| | ||||||||| |||||||||||||| |||||||| || ||   |||| | |||||  || |   ||||||| |   
tcctctaggaaatgcagtttactatggtgga-cagtc--tgcatacctttctgcctttttcctgaaac-tcccaactaa-tatatccgggtgttaataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGACATACTGAAAGAGTTCGCTGCTCA-ACAAGACGACGACCTGTAGAATACAG
















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|88475421|gb|CI412692.1|CI412692
EST:     GGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: GGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88490730|gb|CI428002.1|CI428002
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88515215|gb|CI442869.1|CI442869
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88478249|gb|CI415520.1|CI415520
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88835151|gb|CI370454.1|CI370454
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|86903334|gb|CI313697.1|CI313697
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATTTTATTAA-GTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88469583|gb|CI406854.1|CI406854
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88520955|gb|CI448609.1|CI448609
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88548156|gb|CI477074.1|CI477074
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|38480777|gb|CF964866.1|CF964866
EST:     TGGTTTTTGGGGCAGCTATAGGAAATTATCTTGCACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: TGG-TTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88479544|gb|CI416815.1|CI416815
EST:     CAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|86493201|gb|CI135834.1|CI135834
EST:     CTGGTTTTGGGGCAGCTATAGCAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACCAAGGAAGA
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATA-CAAGGAAGA
EST: gi|8856634|gb|AU093952.1|AU093952
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88273265|gb|CI388721.1|CI388721
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|88225239|gb|CI225155.1|CI225155
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
EST: gi|44676323|gb|CR289757.1|CR289757
EST:     CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAG                         GTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT
genomic: CTGGTTTTGGGGCAGCTATAGGAAATTATCTTGTACATGAGACGGCTCAGgtatttcatt ... taaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcattagccttaatcgttggagctaaatattctcttttggtgtaaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGATATACTGAACGAATTTTTGCTTACACAAGGGGATGGAGTGTAGAACATCA
                       agctaaa  putative branch site (score: 3)
                          taaatattctctttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgtgttcgcattgtactatgaagaaacaactaatgcatcattgtccttcattagccttaatcgttggagctaaatattctcttttggtgtaaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGATATACTGAACGAATTTTTGCTTACACAAGGGGATGGAGTGTAGAACATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - -atgcatc
- - - - - - - - - - - - - - - - - - - - - - tccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggagct