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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCAGAGTCAAGGAGCTCAGAAGCATTTGTTGCACTCTGTCTTCTTACGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACAgtacgtcattaaaacattttgaagtgatagtcacgtttagtttatgattttcctgtctttctgatgtgctcttgttaaacatatgtgtag

Basic information

species Oryza sativa
transcript LOC_Os12g42300.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42300.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G009715_T01 (Zea mays), 5'ss of exon 9
TGTTGCAGAGTCAAGGAGCTCAGAAGCATTTGTTGCACTCTGTCTTCTTACGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACAgtacgtc--attaaaacattttgaagtgatagtcacgtt-tagtttatgattttcctgtctttctgat-gtg---ctcttgttaaacatatgtgtag
|||||||||||||||||| ||||| ||||||||||| |||||||||||||| ||  |||| ||||| ||| |||| ||   | |||||||||||||||||||| ||   |||  || ||||   ||| |||  ||  || |  | | | | |||  ||  ||| |||| ||    ||| ||  |    | | |||||
TGTTGCAGAGTCAAGGAGTTCAGAGGCATTTGTTGCGCTCTGTCTTCTTACAGTCGCAGGGACATCACTTATCACCCAGAAGCTGGGATTTAGTGATACAgtatgttctatttgaaaatttc--agttatatccagattgtgctcttttagttttttggatttatgattgtttacctcctgacatcattctatgtag
















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|29671927|gb|CB668202.1|CB668202
EST:     CGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACA                         TTAGGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACC
genomic: CGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACAgtacgtcatt ... atatgtgtagTTAGGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACC
EST: gi|29626659|gb|CB631670.1|CB631670
EST:     CGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACA                         TTAGGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACC
genomic: CGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACAgtacgtcatt ... atatgtgtagTTAGGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACC
EST: gi|29668944|gb|CB665219.1|CB665219
EST:     CGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACA                         TTACGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACC
genomic: CGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACAgtacgtcatt ... atatgtgtagTTAGGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACC

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), 67 (downstream exon)
Score: 19

TGTTGCAGAGTCAAGGAGCTCAGAAGCATTTGTTGCACTCTGTCTTCTTACGGTTTCAGGAACATCCCTTCTCACGCAATGGTTGGGATTTAGTGATACAgtacgtcatt ... atatgtgtagTTAGGTGCATTTCTGGCTGGGGCCATTCTTGCAGAGACAAATTTCCGTACCCAAATTGAAGCTGACATAAGGCCATTCAGAGGTTTGCTGCTTGGGTTGT




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