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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTGGCGGTGGTTCTGACAATCCACACTTGCCCCATAACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttctaaattattccaaagctgtctattttcaatatcttgtcaagggctgctagcgacacaagcatacaaagaatgctgacgctcttcaaccatgtattcctcag

Basic information

species Oryza sativa
transcript LOC_Os07g43390.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43390.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G013811_T01 (Zea mays), 5'ss of exon 13
CTTTTGGCGGTGGTTCTGACAATCCACACTTGCCCCATAACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttctaaattattccaaagctgtctatttt-caatatcttgtcaagggctgctagcgacacaagcatacaaagaatgctgacgctcttcaaccatgtattcctcag
|||| || |||||||||||||| || || ||||| || ||||||||| | |||||||| || ||||| |||||||| || || || || ||||||||| || || |||   | |||| | | ||   | |   | |  ||| || |||  |                    || | | |      | |            
CTTTCGGAGGTGGTTCTGACAACCCTCATTTGCCACACAACCATGAAATGGATCAAGTTGTGTACACTGGAACACATGATAACGATACAgttagtttcgaactttttcgtcaactgtttttcttattaaaagatctgtaggactactaagggggtgtctggtttctagggactaatgtttagtccctag-----------
















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|86251678|gb|CI016967.1|CI016967
EST:     ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACG                         GTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
genomic: ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
EST: gi|88832166|gb|CI017400.1|CI017400
EST:     ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACG                         GTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
genomic: ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
EST: gi|89186521|gb|CI048193.1|CI048193
EST:     ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACG                         GTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
genomic: ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
EST: gi|89163744|gb|CI100634.1|CI100634
EST:     TGATCAAGTAGTATACACCGGAACACACGACAATGACACG                         GTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
genomic: TGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
EST: gi|88223687|gb|CI223536.1|CI223536
EST:     ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACG                         GTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
genomic: ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT
EST: gi|86504785|gb|CI147418.1|CI147418
EST:     ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACCATGACACG                         GTTATTGGTTGGTGCCAAACTTTACCAGAGGAAGAGAAGCAGACT
genomic: ACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT

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: 75 (upstream exon), 45 (downstream exon)
Score: 39

CTTTTGGCGGTGGTTCTGACAATCCACACTTGCCCCATAACCATGAATTTGATCAAGTAGTATACACCGGAACACACGACAATGACACGgttagtttct ... tattcctcagGTTATTGGTTGGTGGCAAACTTTACCAGAGGAAGAGAAGCAGACT




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