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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatccaaatgagcctgaactgtctttcactaatctgtctaattgtttctactgtatcatacatggtgtcatatgcctttgctgtatattcttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAACGCGGGATCGATCTCAAAGGGCAGGACCAGCTCCAGAGGCTAATGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g27020.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 5
--ccatccaaatgagcctgaactgtctttcactaatctgtctaattgtttctactgtatcatacatggtgtcatatgcctttgctgtatattcttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAACGCGGGATCGATCTCAAAGGGCAGGACCAGCTCCAGAGGCTAATGCAGAG---
    |  ||        | ||       |||||   |     |   ||      | |||    | |  ||| |   |  | || |      ||    | ||| |||||||| |||||||||||||| |||||   |   |||||||||||| | || ||||||||||  ||||| |||||||| ||||| ||||||||||||   
gcttaaacatcctcttttcaatcaagagtcactgcaccagtaagcagtaaaggatatattcatctt--tgtaactagtttatgtttctgtgtcacccttcagACTACGAGCGGCTGCAAAGGCCAAGGGAGAACAG---AAAAGGACTCGACCACGTGATCGATCTCGGAGGGCTGGACCAGCACCAGAAGCTAATGCAGAGATT
















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|29688505|gb|CB684780.1|CB684780
EST:     AGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: AGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
EST: gi|88688419|gb|CI731995.1|CI731995
EST:     CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
EST: gi|88689180|gb|CI732756.1|CI732756
EST:     CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
EST: gi|29665377|gb|CB661652.1|CB661652
EST:     AGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: AGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
EST: gi|2443097|gb|C74868.1|C74868
EST:     CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
EST: gi|29672001|gb|CB668276.1|CB668276
EST:     CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
EST: gi|29625908|gb|CB630919.1|CB630919
EST:     CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAG                         GCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC
genomic: CCACCAAGTAAGGAGATGGATGCTAAGATGAGAGATGAGGAAGCTAGAAGgtttgttggg ... cttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctactgtatcatacatggtgtcatatgcctttgctgtatattcttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAACGCGGGATCGATCTCAAAGGGCAGGACCAGCTCCAGAGGCTAATGCAGAG
                                           ttcttattcc  CT-rich tract
                                     tgtatattcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatccaaatgagcctgaactgtctttcactaatctgtctaattgtttctactgtatcatacatggtgtcatatgcctttgctgtatattcttattccagGCTACGAGCAGCTGCAAAGGCCAAAGGAGAGGGGGTAAAAAGGACTCGAACGCGGGATCGATCTCAAAGGGCAGGACCAGCTCCAGAGGCTAATGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC