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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCAACGCCGAGGATATGGTGAAGAGGAACAAATCCGGCCAGCCACAGCTTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcagagcaggatctaggcttggactatgctccctaatcccaatttaacctgctttgctgcatgcctgtgttgattttaatcttgctggttctatgtgtgaatttattatag

Basic information

species Oryza sativa
transcript LOC_Os05g40420.1
intron # 9
splice site 5'
intron type U2

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|88839805|gb|CI017570.1|CI017570
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|86524793|gb|CI164999.1|CI164999
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCTTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88434513|gb|CI501939.1|CI501939
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|86592517|gb|CI253198.1|CI253198
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89168322|gb|CI109526.1|CI109526
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|87022092|gb|CI259164.1|CI259164
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|218482759|gb|FG947255.1|FG947255
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|94362155|gb|CI052472.1|CI052472
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88992023|gb|CI035161.1|CI035161
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|87026872|gb|CI259525.1|CI259525
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|86478225|gb|CI120858.1|CI120858
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|86889118|gb|CI315729.1|CI315729
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|86251274|gb|CI055407.1|CI055407
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88837678|gb|CI079038.1|CI079038
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88847922|gb|CI006108.1|CI006108
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|8527713|gb|AU092528.1|AU092528
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACTTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|55409364|gb|CV721740.1|CV721740
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|3763744|gb|AU030496.1|AU030496
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|38475605|gb|CF959738.1|CF959738
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89198567|gb|CI016652.1|CI016652
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|58592226|gb|CF990534.1|CF990534
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88245573|gb|CI245422.1|CI245422
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|33812548|gb|CF332162.1|CF332162
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTTTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89173758|gb|CI041651.1|CI041651
EST:     TTGACCAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|87024582|gb|CI259297.1|CI259297
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89188086|gb|CI115335.1|CI115335
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89192294|gb|CI049755.1|CI049755
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89175858|gb|CI042879.1|CI042879
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|29684030|gb|CB680305.1|CB680305
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|8858162|gb|AU095480.1|AU095480
EST:     GACAAGAAAGGCGAAATCCCAGATTTCTTACCTCACACACTCTTCAGCCA                         GTGCCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCG
genomic: GACAAGAAAGGCGAAAT-CCAGA-TTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTG-CCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCG
EST: gi|86261542|gb|CI017284.1|CI017284
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89195422|gb|CI051535.1|CI051535
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89194679|gb|CI117116.1|CI117116
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88215087|gb|CI214936.1|CI214936
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88991606|gb|CI019784.1|CI019784
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88990572|gb|CI107959.1|CI107959
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|88216968|gb|CI216672.1|CI216672
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|86420372|gb|CI056361.1|CI056361
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
EST: gi|89175355|gb|CI042376.1|CI042376
EST:     TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCA                         GTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC
genomic: TTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 64 (downstream exon)
Score: 26

TGGCAACGCCGAGGATATGGTGAAGAGGAACAAATCCGGCCAGCCACAGCTTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcag ... tttattatagGTGCCAGTTGCCATTGGAGGCCCTGGCCTACATTCTGGGGTGAGATTCCGCAACGACGTGCAGACCCCTGGCCTCGCCAACGTCGCCGCCACCGTGATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCAACGCCGAGGATATGGTGAAGAGGAACAAATCCGGCCAGCCACAGCTTGACAAGAAAGGCGAAATCCAGATTCTTACCTCACACACTCTTCAGCCAgtaagtgcagagcaggatctaggcttggactatgctccctaatcccaatttaacctgctttgctgcatgcctgtgttgattttaatcttgctggttctatgtgtgaatttattatag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA