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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGAAGCACTGGAGGGTTGAACAATATTAGCAACGATAACTCCGCTACTGATTCAAAGGACTTGCGTGCTAAGgtttactgcacattttgccctttattactacaataatgcctctatatcatgttactagcagctttctttaacgtgtccatccttttgatgttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g05740.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 3
CTCGAAGCACTGGAGGGTTGAACAATATTAGCAACGATAACTCCGC---TACTGATTCAAAGGACTTGCGTGCTAAGgtttactgcacattttgccctttat-tactacaataatgcc--tctatatcatgttactagcagctttctttaacgtgtccatcct--tttgatgttgtag
|| |||  ||||||||| |||||| ||| |||||||||| |||  |     |   |||||||||||||||||||||||||  |   ||    | | || ||  |  |  ||| |||    |  || |||| ||  ||      ||||||    ||    || |  |||    |||   
CTAGAAATACTGGAGGGCTGAACACTATCAGCAACGATAGCTCTCCAGACGCCAGTTCAAAGGACTTGCGTGCTAAGgttagccaaactccatcctctctaccttttgtaattatggtggttgatctcatatt-ttatttcacttcttttggttgcttgtcttggtttagaattggtt
















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|3760086|gb|C97344.1|C97344
EST:     ATATTAGCAACGATAACTCCGCTACTGATTCAAAGGACTTGCGTGCTAAG                         TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGC
genomic: ATATTAGCAACGATAACTCCGCTACTGATTCAAAGGACTTGCGTGCTAAGgtttactgca ... gatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGC
EST: gi|6782805|gb|C99985.1|C99985
EST:     CTCCGCTACTGATTCAAAGGACTTGCGTGCTAAG                         TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGC
genomic: CTCCGCTACTGATTCAAAGGACTTGCGTGCTAAGgtttactgca ... gatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGC
EST: gi|300216317|gb|HO088102.1|HO088102
EST:     ATACTAGCAACGATAACTCCGCTACTGATTCAAAGGACTTGCGTGCTAAG                         TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGC
genomic: ATATTAGCAACGATAACTCCGCTACTGATTCAAAGGACTTGCGTGCTAAGgtttactgca ... gatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGC

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: 73 (upstream exon), 54 (downstream exon)
Score: 43

CTCGAAGCACTGGAGGGTTGAACAATATTAGCAACGATAACTCCGCTACTGATTCAAAGGACTTGCGTGCTAAGgtttactgca ... gatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG




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