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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatactaaagttttggcagccccactgaacccaagaaacaaaaaggatagacaaatgggtactttctttctcatatgctgatgtggtttttgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTTGAAGAAGGTTCGGGTTGGTGAAGAAATTTCTTTGGTCAG

Basic information

species Oryza sativa
transcript LOC_Os11g36070.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G104449_T02 (Zea mays), 3'ss of exon 5
-----------tatactaaagttttggcagccccactgaacccaagaaacaaaaaggatagacaaatgggtactttctttctcatatgctgatgtggtttttgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTTGAAGAAGGTTCGGGTTGGTGAAGAAATTTCTTTGGTCAG
           | |   | | |||  | |     | | ||||     || | |||||| | | | || |        | | ||||   ||||||  |||||| |  ||||||||||||||||||||||| |||||||||| | ||| |||||||||||| ||||| || || ||| |||||||||| |||| | |||||||
caacatgggtctgtgtcataattt-agtattttgagtcaacctggacaaaataaagga-aaaaatatag--------tctttcatgcactgatg-agttttttttctccagGTTTCCACAATACAACCTGCCAACTTTTAGAATTGATCAGTCAGGCTGCTTGAAAAAAGTGCGGATTGGTGAAGAGATTTGTATGGTCAG
















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|29626187|gb|CB631198.1|CB631198
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAG
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAG
EST: gi|29623258|gb|CB628269.1|CB628269
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
EST: gi|29626153|gb|CB631164.1|CB631164
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
EST: gi|29665385|gb|CB661660.1|CB661660
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
EST: gi|29626975|gb|CB631986.1|CB631986
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
EST: gi|29672693|gb|CB668968.1|CB668968
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
EST: gi|29623293|gb|CB628304.1|CB628304
EST:     GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACATGTGTTTCATGGGAATCGTCTCTGTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
EST: gi|25778077|gb|CA752829.1|CA752829
EST:     GTACAAAAAATG                         GTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT
genomic: GTACAAAAAATGgtgagcacat ... tgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagacaaatgggtactttctttctcatatgctgatgtggtttttgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTTGAAGAAGGTTCGGGTTGGTGAAGAAATTTCTTTGGTCAG
                              tgctgat  putative branch site (score: 3)
                                         tttttgt  putative PPT
                 tttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatactaaagttttggcagccccactgaacccaagaaacaaaaaggatagacaaatgggtactttctttctcatatgctgatgtggtttttgtgttccagGTTTCCACAATACAACCTTCCAACTTTTAAAGTTGCTCAGTCAGGCTGTTTGAAGAAGGTTCGGGTTGGTGAAGAAATTTCTTTGGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA