Sequence
atgc intronic sequence ATGC exonic sequencegtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g03440.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 8
gtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
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-----------------------------------------------------------------------------atctgatc--taaacttataa----cgccagtaaaatgtggtgaat-tgcgatggttgagttcattgtgtgggaa--tgaaatctaa-gtgattcccttttctcatgcagTTTTGCCACACAAAGGAGGACTACGAGGAACATGGAGCCAGCATCTGCAGAACAAGCCCCGTTTTCAAAGGAATGTACTGAATTTTTCCTCACGACCCAT
upper sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G305332_T01 (Zea mays), 3'ss of exon 4
gtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA-
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---------------------------------------------------------------------------------cactt-taaagcagtgttataactgag--ctatgaatacaat---tattcctcgtgaattctttttgtgcgaatgaaatctaagtgatctgtcttttctcatgcagTTCTGCCACACAAAGGAGGAATACGAGGAACATGGAGCCAGCATCTGCAGAACAAGCCCGGTTTTCAAAGGAATGTACTGAATTTTCCTCACA-ACCCATC
upper sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA08G13810.1 (Glycine max), 3'ss of exon 8
gtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
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-------------------------------------------------------------aatgtcattctccttgggagtgcccataatttcttaatgtttctttaatccttccaataaatct-cgatgcaagttttaa---------aatttcgggtctaatgtg----------------cagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACGACAAATTAGTTG
upper sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 8
gtgccttccactttacactctttgagtcttgacacctcattctgcaaatttaataatatgacatattctgccatataactttgttaataagtcaataatatgcttcaggtcaatgcaaaccatatgcactgcacacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctcttt-cagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
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-------------------------------------------------------------------atgccat-tctccttgggagt--gtccataatttgtt-------aatgcttcttttaatccttcca-------ataaa-tctcgatgcaagttttacaatatctg---gtccattgtgcagGCTTGTCATACAAAGGCAGAATATGAGGAGTATGGAGCAAGCATTTGCCGGACAAATCCTGTTTTCAAGGGAATGTATTAAATCAACAACAAATTAGTTGMapped 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|86434268|gb|CI094611.1|CI094611EST: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAG AGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
genomic: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAGgtgccttcca ... tctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
EST:
gi|86498030|gb|CI140663.1|CI140663EST: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAG AGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
genomic: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAGgtgccttcca ... tctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
EST:
gi|86872760|gb|CI341970.1|CI341970EST: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAG AGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
genomic: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAGgtgccttcca ... tctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
EST:
gi|88271468|gb|CI387521.1|CI387521EST: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAG AGTTGCCACACAAAGGAAGAATACGAGGAGCATGGACCAAGCATCTGCCGG
genomic: CAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAGgtgccttcca ... tctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGG
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:
45 (upstream exon),
17 (downstream exon)
Score:
3CCTGTTGAAGTCAATGTGGTCGCCCATCCTATACAGAGTTATGCAGCTTGGTTCGGGGGTTCAGTAGCTGCTTCTAACCCTGAATTTTATGAGgtgccttcca ... tctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacgtgaataaagtgataagatggaatctaaagtgtttgtatgttctctttcagAGTTGCCACACAAAGGAAGAATACGAGGAGCATGGAGCAAGCATCTGCCGGACCAGCACCGTTTTCAAAGGGATGTACTGAATTTTTTCCACCTGTCCAA
atctaaa putative branch site (score: 3)
tgttctctttc putative PPT
tgaataaa TA-rich tract