Sequence
atgc intronic sequence ATGC exonic sequenceTGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgcttattgtttgtcatctttgtatttctcccaaaggtattttatgcttagattaattttaactatttaaccttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g24704.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G014136_T01 (Zea mays), 5'ss of exon 9
TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgcttattgtttgtcatctttgtatttctcccaaaggtattttatgcttagattaattttaactatttaacctt-ttcag
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AGGTCAAGGTCTAAAGACTGAGAACCGCATAGGAATTTTCAAATCTGAATTTGATGTCCAGTCCACATTTGAGGGTGATAACAATGTGCTAATGCAGCAGgttattg---ttgttttcagtcatgcatccattt-tatcaaaggtgcttcgtgtgtgg-----ttgtaacaatttaaccttgtttag
upper sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G14060.1 (Glycine max), 5'ss of exon 9
TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgct----tattgtttgtcatctttgtatttctcccaaaggta----ttttatgcttagattaattttaactatttaacctttt-cag-----
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AGGACAAGGAGTTAAATCTGAAAATCGTGTTGGCAATTTCATGGGTGAATTTGATGTGCATTCGACATTTGAGGGGGACAACAATGTTCTAATGCAGCAGgtaaaatgagtattctgttatatatgaaatttgaataataattaagcacaacatttttaaattcaaacctaggagacatgatgagctgattgcaaagcat
upper sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G43840.1 (Glycine max), 5'ss of exon 9
TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgct----tattgtttgtcatctttgtatttctcccaaaggtattttatgcttagatt--aattttaactatttaaccttttcag----------
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AGGACAAGGAGTTAAATCTGAAAATCGTGTTGGCAATTTCATGGGTGAATTTGATGTGCATTCGACATTTGAGGGGGACAACAATGTTCTGATGCAGCAGgtaaaatgaatattctgttaaatatgaaatttgaataataattaa--gcacaacatttttaaattcaaaccttggagacatgatgagctgattgcagagcat
upper sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G06310.1 (Arabidopsis thaliana), 5'ss of exon 9
TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgcttattgtttgtcatctttgtatttctcccaaaggtattttatgcttagattaattttaactatttaaccttttcag
|||||||||||||| ||||| || || |||| ||| |||| |||| |||||| ||| ||||||||||||| ||||||||||| || ||||||| ||| | || | ||| || | || | || || || | || | | | | ||
AGGCCAAGGTTTGAAAACAGAAAACCGAGTAGGTCATTTAAAAGGAGAATATGATGTGCAGACTACATTTGAGGGTGACAATAATGTACTCATGCAGCTGgtaggctaaggaat--ataatcaaaggtgaactttctttgttttgacaatacaatttgacttatcc-attcttatggggaacttag
upper sequence: LOC_Os06g24704.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G06290.1 (Arabidopsis thaliana), 5'ss of exon 9
TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgcttattgtttgtcatctttgtatttctcccaaaggtattttatgcttagattaattttaactatttaaccttttcag-------
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AGGGCAAGGTGTGAAAACAGAAAATCTAGTTGGTCAGTTGAAAGGTGAATTTGATGTGCAGACTACATTTGAGGGTGACAATAATGTATTGATGCAGCAGgtaagcg-gcacattatt-gtgatttgcatgatcaatactgtaaatttccctgttttgaccatacaattttactttaccgttggggaatttagMapped 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|29670183|gb|CB666458.1|CB666458EST: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
EST:
gi|29670228|gb|CB666503.1|CB666503EST: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
EST:
gi|14571492|gb|BI118860.1|BI118860EST: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
EST:
gi|29665965|gb|CB662240.1|CB662240EST: TTGATGTCCAGACTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAG GTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
genomic: TTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAA
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:
58 (upstream exon),
58 (downstream exon)
Score:
21TGGCCAAGGTTTGAAGACAGAGAATCGCATAGGAATTTTCAAAGCTGAATTTGATGTCCAGTCTACATTTGAGGGCGACAATAATGTTCTAATGCAGCAGgttattttgc ... accttttcagGTAAGCAAAGCCCTTTATGCTGAATTTTTGACAGCAAAAAGGAAGAATCAACCATTCAAGGGATTGGGCTTGGAACACTTGAATGGTCCTTGCCCTGTTA
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