Sequence
atgc intronic sequence ATGC exonic sequencegtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g39310.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 5
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
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-------------------------------------------------------------gtatttaccttgggat-----tttctttcttcatatgtgtagGTCATGATGAGGTTGTTCAGTCCTCGCAAAACAACATTGTTGTTTGTTATACGTGACAAATCAAGG
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 7
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactata-atatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
|| | | |||| | | | || | || | ||| | ||| || | |||| | |||| |||| |||||||||||||| |||||||| ||||| ||| |||||||||| || |||||||| |||||
------------gtatcatt-caactacctattgattacaagcaatagtt-tccaatctaaaaagttggtatttatctaattgcatgcttgtatttgctttcagGTCATGATGAGATTGTTTAGTCCACGCAAAACAACAATGTTGTTTGTCATACGTGATAAGACAAAG
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactata-atatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
|| ||| || | | | | || |||| || ||| |||| | || | | || || | | || | |||| |||||||||||||| |||||||| ||||| |||||| ||||||| || ||||||||| ||| |
----gtatgt-gttgttggcctattgactacaagaacttgaatcttgaatcttgaaacttgtcaattgtcatttatttaactgcacactaaattttactttcagGTCATGATGAGATTGTTTAGTCCACGAAAAACAACATTGCTGTTTGTCATACGTGATAAAACAAGG
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 6
gtcagt-ttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
|| || |||| || ||| | | || |||| || ||| ||| || | || | ||| | | | | | |||| |||||||||||||| |||||||| ||||| |||||||||||||| || || |||||| ||| |
gtatgtgttgtcagc-ctattgactacaagcaattatcttgaatcttgaaacttgtcgattgacatttatttaaatgc----acattcattttacttt---cagGTCATGATGAGATTGTTTAGTCCACGAAAAACAACATTGTTGTTTGTCATACGCGATAAAACAAGG
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactata-atatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
|| | | | |||| || | || | || | ||| | ||| || | |||| | |||| |||| |||||||||||||| |||||||| ||||| ||| |||||||||| || |||||||| |||||
------------gtatcattcaataa-cctattgactacaagcaacagtt-tccaatctaaaaagttgttatttatctaattgcatgcttgtatttgctttcagGTCATGATGAGATTGTTTAGTCCACGCAAAACAACAATGTTGTTTGTCATACGTGATAAGACAAAG
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttcagtggtggaagatactataatatcattgtgtctttg---tcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
|| ||| || |||| | ||| | || | | ||| | | || || ||| |||||| | | |||| |||||| ||||||| |||||||||||||| ||| || ||||||| || || |||||| | |
gtattttttttgatgct----caggaagttaaa------aactctttgtgtatcacaaaaatattttcttaccctaagtttgaatctttggagttgggtttggcagGTGATGATGCGATTGTTTAGTCCACGTAAAACAACAATGCTGTTTGTAATACGAGATAAAACCCGG
upper sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 6
gtcagtttgttagtgctacaatgtgggcttattttctttgattcctgattcttc--agtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
||| | || | ||| ||| | | || | | | | | | | | | | | | | | ||||||||||| ||||||| |||||||| ||||| || ||| |||||||||||||||||||| ||| |
----------------------------gtatctctttatgctgacaattattctgaatctcaagagcttcagttgtctaactttatgatgttatatccttacagGTTATGATGCGATTGTTTAGTCCACGAAAAACAACTTTGATGTTTGTTATTCGTGATAAAACAAGGMapped 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|29675672|gb|CB671947.1|CB671947EST: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
EST:
gi|29671821|gb|CB668096.1|CB668096EST: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
EST:
gi|29664221|gb|CB660496.1|CB660496EST: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
EST:
gi|29632288|gb|CB637297.1|CB637297EST: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAG GTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
genomic: TTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATT
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:
64 (upstream exon),
66 (downstream exon)
Score:
61GTGGTGTCATGACATTGGTAGAGAACAGGCTGCGAACAAACCTCTTTTGAAGACTGTTTTCCAGgtcagtttgt ... acctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcagtggtggaagatactataatatcattgtgtctttgtcaacctgaatagGTTATGATGAGATTGTTCAGTCCACGTAAAACGACATTGTTGTTTGTTATTCGTGATAAATCAAAG
atactataatatcatt TA-rich tract