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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTACAAAATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttgttatttttttggaataactttatgagtgaaaaacttgttaatttagaatcgtttactgatttaaagcatcctgcag

Basic information

species Oryza sativa
transcript LOC_Os12g06800.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G039505_T02 (Zea mays), 5'ss of exon 9
CCTGTACAAAATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttgttatttttttggaataactttatgagtgaaaaacttgttaatttagaatcgtttactgatttaaagcatcctgcag
| |||||| |  ||||| |||||||| ||||| ||||||||||| |||||||||||||||||| |  |  || | || ||  |  ||   | |||||| ||||||||     |  ||| | | || |||||| ||||||  |||||
CATGTACAGAGCTCTGCTTCACGGGCGGAACTACACAGGAAAAGCATAGCACAAATGAAGgtttga-taattctgttctttaagaaatagt-tgagtgcaaaacttgcc---tctgaaacatgtattgatttgaagcattttgcag

upper sequence: LOC_Os12g06800.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G468799_T01 (Zea mays), 5'ss of exon 9
CCTGTACAAAATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttgttatttttttggaataactttatgagtgaaaaacttgttaatttagaatcgtttactgatttaaagcatcctgcag----------------------------------------------------------------------
|||| ||| || ||||| |||||||||||||| ||| ||||||| |||||||||||||||||| | |       | || || ||  |   | |||||| ||| ||||     |  ||| | ||||||||||| ||||||  |||||                                                                      
CCTGCACAGAACTCTGCTTCACGGGCTGAACTACACCGGAAAAGCATAGCACAAATGAAGgtttgacactgctctgttctgtaagcatagt-tgagtgcaaagcttgcc---tctgaaacatttactgatttgaagcattttgcagatcaatacacaatctgttcaagatatgcatatatatgctgatccttcacatgttcctgttgttcttatag
















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|33683731|gb|CF311970.1|CF311970
EST:     ATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAG                         ATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGT
genomic: ATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttg ... catcctgcagATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGT
EST: gi|58660828|gb|CK049508.1|CK049508
EST:     TCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAGAAGTGAAG                         ATCAACACGCTGTCCATTCAAGATATGCAAATATATGCAGATCCTTCACG
genomic: TCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACA-AA-TGAAGgttcggcttg ... catcctgcagATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACG
EST: gi|58598143|gb|CK008671.1|CK008671
EST:     GCACAAATGAAG                         ATCAACACGCTGTCCATTCAAGATATGCAAATATATGCAGATCCTTCACGT
genomic: GCACAAATGAAGgttcggcttg ... catcctgcagATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGT
EST: gi|58671021|gb|CK059707.1|CK059707
EST:     ATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAG                         ATCAACACGCTGTCCATTCAAGATATGCAAATATATGCAGATCCTTCACGT
genomic: ATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttg ... catcctgcagATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGT
EST: gi|33683902|gb|CF312141.1|CF312141
EST:     ATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAG                         ATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGT
genomic: ATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttg ... catcctgcagATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGT

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: 40 (upstream exon), 49 (downstream exon)
Score: 18

CCTGTACAAAATTCTGCCTCACGGGCTGAACTGCACAGGAAAAGTATAGCACAAATGAAGgttcggcttg ... catcctgcagATCAACACGCTGTCCGTTCAAGATATGCAAATATATGCAGATCCTTCACGTGTTCCTGTTGTTCTTATAGAACAACATGTCATGGTTGTTCCGCAACATG




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