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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagaaacaaattgtaatttctttaccaactacaatgaatgcatagtgtgggtactaaacatggtgaaatattttttgtcacacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAACGTTGTGAACTTGCTTGAGTCTGCAGCTGATGCTCTCTACAGAAGAGTGA

Basic information

species Oryza sativa
transcript LOC_Os11g42510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42510.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006480_T01 (Zea mays), 3'ss of exon 5
gtcag-aaacaaattgtaatttctttaccaactacaatgaatgcatagtgtgggtactaaacatggtgaaatattttttgtcacacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAACGTTGTGAACTTGCTTGAGTCTGCAGCTGATGCTCTCTACAGAAGAGTGA
||||| || ||  |  | |      | | |  |  |   ||   | |  |||   || | ||      | ||    |||||    || | |||| || ||||| ||||| || |||   |||||| |||| |||||| | || |||||  || |||| |||||||||||||||||||| |||||||||||||
gtcagcaagcagttcttcaaaatgattctacatgtatccaaaaaaaaaggtgaacac-atactgatacagatggaatttgttg-gcacgtagGCGGCGGTTCCCAAGATCCTTTCAGCTGAACACCATGAGTTCCATAGGAATGTTGTTCACCTGCTCGAGTCTGCAGCTGATGCTCTGTACAGAAGAGTGA
















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|29614602|gb|CB619615.1|CB619615
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCGTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|29636664|gb|CB641673.1|CB641673
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|29673666|gb|CB669941.1|CB669941
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|29636535|gb|CB641544.1|CB641544
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|29636663|gb|CB641672.1|CB641672
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|29670359|gb|CB666634.1|CB666634
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|29668799|gb|CB665074.1|CB665074
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
EST: gi|58595127|gb|CF993435.1|CF993435
EST:     CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAG                         GCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC
genomic: CAACAGAAATGCTACTGAATGTGACTTCAGGCCCTGCCTCCATAGTTCAGgtcagaaaca ... acacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatgcatagtgtgggtactaaacatggtgaaatattttttgtcacacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAACGTTGTGAACTTGCTTGAGTCTGCAGCTGATGCTCTCTACAGAAGAGTGA
                 tactaaa  putative branch site (score: 1)
                             tgaaatattttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagaaacaaattgtaatttctttaccaactacaatgaatgcatagtgtgggtactaaacatggtgaaatattttttgtcacacatgcagGCTGCAGTTCCTAAGATTCTCTCAAACGAACACAATGAATTCCATCGAAACGTTGTGAACTTGCTTGAGTCTGCAGCTGATGCTCTCTACAGAAGAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT