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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGCTCTCGGTGCTGCTAAAGGGCTAGCCTTTCTCCATGGAGGTCCCAAACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttcttatcaattcattcacatcatgctcataaatatgttgcacattttcacaagattatttcttgcatgctattctaacagcagtggaaattctgcttatacag

Basic information

species Oryza sativa
transcript LOC_Os06g07230.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g07230.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G410191_T02 (Zea mays), 5'ss of exon 8
GATCGCTCTCGGTGCTGCTAAAGGGCTAGCCTTTCTCCATGGAGGTCCCAAACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttcttatcaattcatt-cacatcatgctcata-aatatgttgcacattttca--caagattatttcttgcatgctattctaacagcagtggaaattctgcttatacag
||| ||||| ||||| || ||||| |||||||| |||||||||||||||||||  || ||||||||||||||||||||||| ||| |||||||||||| |||||| | |||  |||||| ||| || ||  |||  | | |||       || || | |     | | ||||      | || ||  ||||   ||||  ||| | ||| |  ||
GATTGCTCTAGGTGCCGCGAAAGGACTAGCCTTCCTCCATGGAGGTCCCAAACATGTTATTTACAGGGATTTTAAGACATCGAATGTTCTTCTTGATGTGgtactttatctgttcaatttatttcatattgtgcctagacaatgcacgataccttgttaattgtggtgattttacttcttctttttgaacat--gtggtgattttacttctgtag

upper sequence: LOC_Os06g07230.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G446189_T01 (Zea mays), 5'ss of exon 6
GATCGCTCTCGGTGCTGCTAAAGGGCTAGCCTTTCTCCATGGAGGTCCCAAACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttcttatcaattcatt-cacatcatgctcata-aatatgttgcacattttcacaagattatttcttgcatgctattctaacagcagtggaaattctgcttatacag
|||  |||| ||||  || ||||| |||||||| |||||||||||||||||||| |||||||||||||||||||||||||| ||| |||||||||||| |||||| | ||   |||||   || || ||  |||| | | |||       || || | | |   |  |   ||   | || || |   |   ||||  ||| | ||| |  ||
GATTCCTCTAGGTGTCGCGAAAGGACTAGCCTTCCTCCATGGAGGTCCCAAACCTGTAATTTACAGGGATTTTAAGACATCGAATGTTCTTCTTGATGTGgtactttatcagttcaatatgtttcatattgtgcttagacaatgcacgctaccttgtta-attgtggtgattttacttctttttttgaacatgtggtgattttacttctgtag

upper sequence: LOC_Os06g07230.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G007801_T01 (Zea mays), 5'ss of exon 1
GATCGCTCTCGGTGCTGCTAAAGGGCTAGCCTTTCTCCATGGAGGTCCCAAACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttcttatcaattcatt-cacatcatgctcata-aatatgttgcacattttcacaagattatttcttgcatgctattctaacagcagtggaaattctgcttatacag
||| ||||| ||||| || ||||| |||||||| |||||||||||||||||||| || ||||||||||||||||||||||| ||| |||||||||||| |||||| | |||  |||||   || || ||  |||| | | |||   |   || || | |  ||      | || | |  | || | |  |  ||||  ||| | ||| |  ||
GATTGCTCTAGGTGCCGCGAAAGGACTAGCCTTCCTCCATGGAGGTCCCAAACCTGTTATTTACAGGGATTTTAAGACATCGAATGTTCTTCTTGATGTGgtactttatctgttcaatctgtttcatattgtgcttagacaatgcatgctaccttgttaatagtggtgattttacttctttttttgaacgt-gtggtgattttacttctgtag

upper sequence: LOC_Os06g07230.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G014596_T01 (Zea mays), 5'ss of exon 4
GATCGCTCTCGGTGCTGCTAAAGGGCTAGCCTTTCTCCATGGAGGTCCCAAACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttcttatcaattcatt-cacatcatgctcata-aatatgttgcacatt-ttcacaagattatttcttgcatgctattctaacagcagtggaaattctgcttatacag
||| | ||| ||||| || |||||  ||||||| |||||||||||||||||||| || ||||||||||||||||||||||| ||| |||||||||||| |||||| | |||  |||||   || || ||  |||| | | |||       || || || |      |  || |       | || |||||   ||||  ||| | ||| |  ||
GATTGTTCTAGGTGCCGCGAAAGGAGTAGCCTTCCTCCATGGAGGTCCCAAACCTGTTATTTACAGGGATTTTAAGACATCGAATGTTCTTCTTGATGTGgtactttatctgttcaatctgtttcatattgtgcttagacaatgcacgctaccttgttaattgtggtgattttacttcttttttttaacat--gtggtgattttacttctgtag

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|66914151|gb|CX100999.1|CX100999
EST:     CCAGTAATTTACNAGGCATTTTAATGACATCAAATATTCTTCTTGATGCG                         GAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
genomic: CCAGTAATTTAC-AGGGATTTTAA-GACATCAAATATTCTTCTTGATGCGgtactatttc ... gcttatacagGAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
EST: gi|29677837|gb|CB674112.1|CB674112
EST:     AACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCG                         GAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
genomic: AACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttc ... gcttatacagGAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
EST: gi|2801055|gb|AA754349.1|AA754349
EST:     AACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCG                         GRGTACAATGCAAAACTTTCAGATTTKGGGTWAGCGAA
genomic: AACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttc ... gcttatacagGAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAA
EST: gi|29642958|gb|CB647965.1|CB647965
EST:     AACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCG                         GAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
genomic: AACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttc ... gcttatacagGAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
EST: gi|29671665|gb|CB667940.1|CB667940
EST:     GGATTTTAAGACATCAAATATTCTTCTTGATGCG                         GAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA
genomic: GGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttc ... gcttatacagGAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAA

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: 70 (upstream exon), 73 (downstream exon)
Score: 19

GATCGCTCTCGGTGCTGCTAAAGGGCTAGCCTTTCTCCATGGAGGTCCCAAACCAGTAATTTACAGGGATTTTAAGACATCAAATATTCTTCTTGATGCGgtactatttc ... gcttatacagGAGTACAATGCAAAACTTTCAGATTTTGGGTTAGCGAAAGCTGGTCCTCAAGGCGATAAAACTCATGTCTCTACACGGGTTGTCGGTACCTATGGTTATG




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