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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATTGTTTATAACTATCCCAAAGAAATAAAGGCATTTTATATGAGACTCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataaatatttcagacttctagttagttccaatataggttaggtgtaagcatgtaaatgtgttgcatgaacataaattttgaggttaggtgtaat...

Basic information

species Oryza sativa
transcript LOC_Os01g27520.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27520.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G083836_T01 (Zea mays), 5'ss of exon 4
GGTGATTGTTTATAACTATCCCAAAGAAATAAAGGCATTTTATATGAGACTCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataaatatttcagacttctagttagtt-ccaatataggttaggtgtaagcatgtaaatgtgttgcatgaacataaattttgaggttaggtgtaat-------------------------------------------------------------------------
 || ||||| ||||||||||| |||| |||||||||||||||||||||||||||||||||| | ||||| || ||||| ||||||||||||||||| |||||  |  ||||  | ||| || || |     || |   ||   ||      | ||   |  |     |    ||  ||    ||||   || || || |||                                                                         
AGTTATTGTCTATAACTATCCGAAAGGAATAAAGGCATTTTATATGAGACTCAATGATGATGACAAGACGGTGGCTGCAATGGATGTTCTTGTGCCTAAGgtgtagctaaacttctcatacatcaaacctattgctggtaccagtgctccatgagtg-gggagcaaatgatttggcca---gtttttgagtcag-tggaatatccgtttatttaactgctgattttacctttttatgtttataatcatttttgtgctggaatgtttatttcaag
















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|88836360|gb|CI078257.1|CI078257
EST:     TGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|5003639|gb|AU068788.1|AU068788
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAA
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAA
EST: gi|88503370|gb|CI430876.1|CI430876
EST:     ATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: ATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|87020011|gb|CI299409.1|CI299409
EST:     GAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: GAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|66912938|gb|CX099786.1|CX099786
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGCGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|58683506|gb|CK072193.1|CK072193
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|29630322|gb|CB635331.1|CB635331
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGCGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|29620154|gb|CB625166.1|CB625166
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGCGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|88515783|gb|CI443437.1|CI443437
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACNTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|5003638|gb|AU068787.1|AU068787
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|89198769|gb|CI003506.1|CI003506
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|29614514|gb|CB619527.1|CB619527
EST:     TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGCGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: TCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
EST: gi|58688377|gb|CK077064.1|CK077064
EST:     GTAGCTGCTATGGATGTTCTTGTGCCCAAG                         GTTGGCGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC
genomic: GTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataa ... tcttccaaagGTTGGTGAGTTGGTTGGTGGAAGCCAAAGGGAGGAACGTCTGGACCTTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGATTGTTTATAACTATCCCAAAGAAATAAAGGCATTTTATATGAGACTCAATGATGATCAGAAGACTGTAGCTGCTATGGATGTTCTTGTGCCCAAGgtaaatataaatatttcagacttctagttagttccaatataggttaggtgtaagcatgtaaatgtgttgcatgaacataaattttgaggttaggtgtaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT