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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt...

Basic information

species Oryza sativa
transcript LOC_Os03g20310.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 5
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgactt-ctggtctccgcac-caactaaggatgcacatccatatt
|| ||||| |||||||| |||||||||||||| ||||| |||||||||||||| ||||||||| ||| | ||   || |    |||  |    |   ||| |   |   |||     ||  |  ||    |  |||  ||  || |   || |     | | 
GTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGGAAAAGTCGGCTGAGGAAAAAGgtattattagcatggctgtgca-cat-ctgggagctatttctacaattttggtgcagtgtgtcactcccttatgcatgcatgtatgtgcgcgcgctagtgtg

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 5
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgt-catattacctgtccttttttggacaatggaat-tatgacttc-tggtctccgcaccaactaaggatgcacatccatatt
|| ||||| |||||||| |||||||||||||| ||||||||||| |||||||| ||||||||| ||| | ||  ||| | |   | |   | || | | |   |      || | | | | ||| | || |    |||     || |    |   |    || 
GTTTTACGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGCCGGCTGAGGAAAAAGgtattattagcatgactgtgtacacctgggatctattcctacatttttggtgcagtgtgtcactccctgatgcatgcatg---tatgtgcactagtgtgaatc

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 5
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtac-----tataaccaca-actttttgtcatattacctgtccttttt--tggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt
    | ||  |||||||||| ||||||||||| ||||||||||||||| ||||||| || |||      | ||   ||| | |||||||  || ||  |||  ||     || | |      || ||  ||||  | ||  ||   | |||  ||    ||       
ACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAAgtaggaatatgtacttacatattttttgt--taatatttgttgttacaagtgtatatcatttttctgttttcttctttctccatataataaatattactatg------

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 7
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgta----ctataaccacaacttt--------ttgtcatattacc-tgtccttttttggacaatggaattatgacttctggtctc----cgcaccaactaaggatgcac-atccatatt----------------------------------------
   ||| | |||||||||||||||||||||||||| || ||||| || ||||| |||||||||    || |      || |||        |||  | ||||   ||   |   ||||  | | |    ||   |  |  | |     | || ||||| |  |||    ||  |||||                                        
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttctgttaattttagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattgagacccaacaacttatcatgttttataaatatttctgaacttcttttttaaatccttgtttctattcattcag

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA19G31050.3 (Glycine max), 5'ss of exon 7
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgta----ctataaccacaactttttgtcatattacctgtccttttttggacaa-tggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt---------------------------------------------------
   ||| | |||||||||||||||||||||||||| || ||||| || ||||| |||||||||    || |  |   || |||   | |  ||         || |   | |  | |  || |   |     | ||   |   |      ||       ||| ||                                                   
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttccgttaattttagatgaacttgtaaaattattgtgatataggttggtttgttgttcaatatgtcattattgagacccaataatttgtcatgttttatatatattttttgacttattttttaaatccctctttctattcattcag

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 2
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgacttctggtctccgcacca-actaaggatgcacatccatatt----------------------------------------------------------
   ||| | |||||||||||||||||||||||||| || ||||| || ||||| |||| ||||         |   |  ||||      || ||     || | |   ||  || |  |     || ||       || | ||  ||  | || | |  |                                                           
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATGgtaaggccttttctgttaattgtagatgaacttggaaaattattg-tgatataacttggttagttgttcaatatgtcatattattgagacccaacaacttgtcatgttttataaatatttctgaacttcttttttaaatccttgtttctatttattcag

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 5
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttgg-acaatggaat-tatgacttctggtctccgcaccaacta-aggatgcacatccatatt
    | ||  |||||||||| ||||| ||||||||||||||||||||| ||||||| || ||   |  |  |     ||   | || ||   |    ||| |||  ||||  | || | |   ||||| | ||  |     | | |  ||  | ||   ||| 
AGTCTCCGGAGGCTTGCTCAGAATCGCGAGGCTGCAAGAAAAAGTCGGTTGAGAAAGAAAgt---aggaatatgtacttacataatttttgttaatatttgttgatacaagtgtatatcttttttctgttttcttctttctccatataattaatattactatg

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 5'ss of exon 5
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccat-att------------------------------
    | ||  |||||||||||||||||||||| |||||||||||  |  |||| || |||||| | ||       |||||  || | ||   ||   ||| ||  | | |    ||||   | || ||     | | |   ||| ||    |||  | |||                              
ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAGgta-tgtatattttgcttttgttcttgtt--ttgatttttcttatatattcctcttat--ttccttgtaatatctctag--aagaatatctatctgtcattaccttaagcatgttattgtttcctccatag

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 7
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt----------
    | ||  ||||||||||||||||||| |||||| ||||||| ||  ||||||| || |||          |  || ||||   |||   | | |||| |||   | |  ||| | |   | |||||    ||| |   ||   | |  |    || |          
ACTCTTCGTAGGCTTGCTCAAAATCGTGAAGCTGCACGAAAAAGCCGATTGAGAAAGAAAgta-------tgtattttgttgtttaattg--tattctttcttgctaatttaaatca-gctatttggtcagttcacaagtgaaaatttctgaattttagtagagaatatt

upper sequence: LOC_Os03g20310.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 6
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtac-tataaccacaactttttgtcatattacctgt---ccttttttggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt---------------------------------------------------------------------------------------------
   |||||||||||||||||||||||||| ||||| |||||||| ||  | || |||||||||  |      |  |  |    ||| |||   |||   | |  |||  ||  |    ||       |||   | |  |       |   || |  |     ||                                                                                             
ACATTACGCCGGCTTGCTCAAAATCGTGAAGCTGCCAGAAAAAGCCGATTAAGGAAAAAGgtaggtcctgttatgaaatgagttcacatttgatgtagacatcattttcactgttatgttgcacaaactgagtttctaagtgttggatagtgtattttttggttatggtttattctgtctcattttcactgttatgttacacaaacctgggagtgcattgtgtgcactaaatccctttttttggtttctctctttag

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|29622238|gb|CB627249.1|CB627249
EST:     GGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG                         GCATATGTACAACAATTAGAGAGCAGTAAGCTGAAACTTGCAAGCTTGGAG
genomic: GGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataac ... ccttttcaagGCATATGTACAACAATTAGAGAGCAGTAAGCTGAAACTTGCAAGCTTGGAG
EST: gi|58592490|gb|CF990798.1|CF990798
EST:     GGCTTGCTCAGAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAG                         GCATATGTACAACAATTAGAGAGCAGTAAGCTGAAACTTGCAAGCTTGGAG
genomic: GGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataac ... ccttttcaagGCATATGTACAACAATTAGAGAGCAGTAAGCTGAAACTTGCAAGCTTGGAG
EST: gi|5803454|gb|AI978424.1|AI978424
EST:     GGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGNNAAAAANN                         NCATATGTACAACAATTAGAGAGCAGTAAGCTGAAACT
genomic: GGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataac ... ccttttcaagGCATATGTACAACAATTAGAGAGCAGTAAGCTGAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTACGCCGGCTTGCTCAAAATCGTGAGGCTGCAAGAAAAAGTCGGCTGAGAAAAAAGgtactataaccacaactttttgtcatattacctgtccttttttggacaatggaattatgacttctggtctccgcaccaactaaggatgcacatccatatt

- - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - -  AAGAAA