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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTTGGCGCCAGGCGTTGGCTTGCGACGCTGCAGCGCCAATGCGAATGCCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaattctgaacctctacttgccattttccatctaaaacgagctcaatttgcggaatcaactgtgcgcaaattttgcatggaattcatttcggt...

Basic information

species Oryza sativa
transcript LOC_Os02g45250.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45250.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G026643_T01 (Zea mays), 5'ss of exon 7
GCCTTTGGCGCCAGGCGTTGGCTTGCGACGCTGCAGCGCCAATGCGAATGCCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaattctgaacctctac-ttgccattttccatctaaaacgagctcaatttgcggaatcaactgtgcgcaaattttgcatg-gaattcatttcggt-
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GCCTTTGGGGCCAGGCGGTGGCTTGCAATGCTGCAGCGCCAGTGCGAATGCCTGGCCATACTCATGTCCCCTGATACAGTTTCAGCTAATGACTCGTCAGgtacagcaaagtctgaacttttttgttgctattttccatgtacagcctg--taatggactgtgcctac-atatatagtcagtgcaaacgattttttttttgtt
















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|58668045|gb|CK056731.1|CK056731
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCAAACGAAGCATGCTGAAGCTGGCACGCCGGATGA
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGA
EST: gi|58666494|gb|CK055180.1|CK055180
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCAAACGAAGCATGCTGAAGCTGGCACGCCGGATGA
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGA
EST: gi|58654235|gb|CK042915.1|CK042915
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCAAACGAAGCATGCTGAAGCGGGCACGCCGGATGA
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGA
EST: gi|58604792|gb|CK015320.1|CK015320
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCAAACGAAGCATGCTGAAGCTGGCACGCCGGATGA
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGA
EST: gi|7273764|gb|AU062749.2|AU062749
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCAAGCGAAN-ATGCTGAAGCTGGCACGCCGGATGA
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGA
EST: gi|58598705|gb|CK009233.1|CK009233
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCAAACGAAGCATGCTGAAGCTGGCACGCCGGATGA
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGA
EST: gi|58655855|gb|CK044535.1|CK044535
EST:     CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTG                         CTATATCGCAAGAGGGCG-GACGAAGCATGCTGAAGCTGGCACGCCGGATG
genomic: CCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAG-CGAAGCATGCTGAAGCTGGCACGCCGGATG

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: 56 (upstream exon), 69 (downstream exon)
Score: 6

GCCTTTGGCGCCAGGCGTTGGCTTGCGACGCTGCAGCGCCAATGCGAATGCCTTGCCATCCTCATGTCCTCTGCTACAGTGACAGCAAATGACTCGACTGgtacaggaaa ... atgcatgcagCTATATCGCAAGAGGGCAAGCGAAGCATGCTGAAGCTGGCACGCCGGATGACGGAGAACTTCTGTGCTGGGGTGAGCGCATCGTCTGCACGTGAATGGAG




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