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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGTGACATCCACAGACTTGAGTTCGAGGAGCTATCTGAAGAGTGCAAGCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttactttgctgcctgaaatttgtctatgattcttataagtcggcaaagttgcatagctatgcacgatcgaacaaaagtataagaaatgatgcgtgaaaagaaaaggaattgactggtttgttgcataggtagtaactccatttccctttgcatttcccttttgtttttgctatcctttag

Basic information

species Oryza sativa
transcript LOC_Os06g49430.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49430.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G306028_T02 (Zea mays), 5'ss of exon 10
---TGGTGTGACATCCACAGACTTGAGTTCGAGGAGCTATCTGAAGAGTGCAAGCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttactttgctgcctgaaatttgtctatgattcttataagtcggcaaagttgcatagctatgcacgatcga-acaaaagtataagaaatgatgcgtgaaaagaaaaggaattgactggtttgttgcataggtagtaactccatttccctttgcatttcccttttgtttttgctatcctttag
    | ||||| |||||||  ||| || ||  ||||||| ||||||||||| ||||| ||||||||||||||||||| || || |   || ||| | || |||||| || |              ||||   ||     | |   |||| ||||  |  ||| |  | ||||| |||          | |     |||    |     | |     |||                                                                       
GAGCGATGTGAAATCCACAAGCTTAAGCTCTCGGAGCTACCTGAAGAGTGCGAGCATAAGTGCTTCCAAGTGTGTCGTTGCCACG---AAGAAACACCCGGAGgtaatgctg-------------aattcaact---ggtgtggcaagtaggcagggcggcacacttgtgcactatcagtgtcttcctctttttgatggcatgcatgcacactgtcaat-----------------------------------------------------------------------
















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|29627484|gb|CB632495.1|CB632495
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|88245478|gb|CI245327.1|CI245327
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|86859816|gb|CI345452.1|CI345452
EST:     TAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: TAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|88217018|gb|CI216722.1|CI216722
EST:     CAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: CAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|38470682|gb|CF954813.1|CF954813
EST:     GGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGTGGTCGTGTCGATGGATTGTCTG
genomic: GGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAG-GGTCG-GTCGATGGATTGTCTG
EST: gi|86528043|gb|CI168249.1|CI168249
EST:     TTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: TTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|27577996|gb|CB000691.1|CB000691
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|86429445|gb|CI076126.1|CI076126
EST:     TAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: TAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29681151|gb|CB677426.1|CB677426
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29672762|gb|CB669037.1|CB669037
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|86481501|gb|CI124134.1|CI124134
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|117380082|gb|BI892449.2|BI892449
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|88247067|gb|CI246916.1|CI246916
EST:     CAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: CAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|88247130|gb|CI246979.1|CI246979
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|25803435|gb|CA759404.1|CA759404
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29632341|gb|CB637350.1|CB637350
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|86500328|gb|CI142961.1|CI142961
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|89195898|gb|CI007317.1|CI007317
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|58694508|gb|CK083195.1|CK083195
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29645355|gb|CB650362.1|CB650362
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|58682915|gb|CK071602.1|CK071602
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|88201577|gb|CI201932.1|CI201932
EST:     AAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: AAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|58603200|gb|CK013728.1|CK013728
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|86829561|gb|CI286751.1|CI286751
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29646573|gb|CB651580.1|CB651580
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTTTGAAGAAATGGAAGGGTCGGTCGATGGATTGTTTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|86851880|gb|CI316449.1|CI316449
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29646572|gb|CB651579.1|CB651579
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
EST: gi|29633814|gb|CB638823.1|CB638823
EST:     GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAG                         GATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA
genomic: GCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttac ... tatcctttagGATGATTACATCTCTGAAGAAATGGAAGGGTCGGTCGATGGATTGTCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGTGACATCCACAGACTTGAGTTCGAGGAGCTATCTGAAGAGTGCAAGCATTAGTGCTTCCAAGTGTGTCGCTGTCAAGGACAATAAAGAACCAGAGgtactgttactttgctgcctgaaatttgtctatgattcttataagtcggcaaagttgcatagctatgcacgatcgaacaaaagtataagaaatgatgcgtgaaaagaaaaggaattgactggtttgttgcataggtagtaactccatttccctttgcatttcccttttgtttttgctatcctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC