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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTTGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggactgtgacaatgtttactttcaataagactgcttagaagttcactctaaataattttctttatcttgatgtgaactatttgataggatgcag...

Basic information

species Oryza sativa
transcript LOC_Os05g01250.1
intron # 6
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|88547948|gb|CI478279.1|CI478279
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|55411056|gb|CV723432.1|CV723432
EST:     GCCTGCTGCACCAACGGGTCACACACCCGCGCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: GCCTGCTGCACCAACGGGTCACACACCCGC-CCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|33655179|gb|CF277793.1|CF277793
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|33662788|gb|CF293755.1|CF293755
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88540264|gb|CI470295.1|CI470295
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|29687110|gb|CB683385.1|CB683385
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|27576216|gb|CA998910.1|CA998910
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88472180|gb|CI409451.1|CI409451
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88486183|gb|CI423454.1|CI423454
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|5003511|gb|AU068660.1|AU068660
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88535886|gb|CI465601.1|CI465601
EST:     TTCCTGCTGCACCCACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|33689676|gb|CF317915.1|CF317915
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|33655395|gb|CF278009.1|CF278009
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|117224782|gb|CT845909.1|CT845909
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|86870086|gb|CI318007.1|CI318007
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88836570|gb|CI010826.1|CI010826
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88834968|gb|CI370271.1|CI370271
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|27577821|gb|CB000516.1|CB000516
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88470654|gb|CI407925.1|CI407925
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88505656|gb|CI433162.1|CI433162
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88964831|gb|CI084829.1|CI084829
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
EST: gi|88507718|gb|CI435224.1|CI435224
EST:     TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAG                         GAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA
genomic: TGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGA

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: 69 (upstream exon), 72 (downstream exon)
Score: 9

CTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTTGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggac ... gttggtgcagGAGGACGAATTGGGATTGCCGACAGTGCCACAAGCATCGATCCGTAGTTGATTGGATTCGTTTTGTAAAAACATAATGTCGTATGCAATAACAAATTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGTACCTTCAACCAGATAAGGAATCAGATCTAGATTCTGAGCTTAACTTGCCTGCTGCACCAACGGGTCACACACCCGCCCCACCAAACCGGCAGCAGgtacatggactgtgacaatgtttactttcaataagactgcttagaagttcactctaaataattttctttatcttgatgtgaactatttgataggatgcag

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