Sequence
atgc intronic sequence ATGC exonic sequencegtattttatacaccgcttccgtcatgttgtgtgccatatgaccatcatgggttctcatagaagttttttttgtttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g09246.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 4
gtattttatacaccgcttccgt------catgttgtgtgccatatgaccatcatgggttctcatagaagttttttttgtttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
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gtacttcataccttttctgcatagataacatcttgaatgccatgc-acctcca-gaattctgataaaaaaatga--taattac-acagGTCATTGAAACTAATAGGGCTGAAGAGTCACAAGGTCATGTACACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
upper sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 16
gtattttatacaccgcttccgtcatgttgtgtgc-catatgaccatcatgg-gttctcatagaagttttttttg---tttgt-----tgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
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gtccataactaacttccttgtgaatttcagggatactcattacctttggaatgttaccatcaaatttaactttgaattttgtgagctttcagATTATGGAAACAAACAGAAGTGAGGAATCTCCGAGTCATGTGCACAGGTTGTATTTCCAGGGCCCAAATACATTCAGTGAACCTTGGCATCTACCTCATT
upper sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------gtattttatacaccgcttccgtcatgttgtgtgccatatgaccatcatgggttctcatagaagttttttttgtttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
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agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacact-ccttatattacagtgttgtgctgctgtttataatgttattctttgt--cagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACAMapped 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|58598030|gb|CK008558.1|CK008558EST: CAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAG GTCTTGGAAACTAGTGGGGCTGAGGAATCGCATGGGCATGTACACAGGATG
genomic: CAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAGgtattttata ... tttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATG
EST:
gi|58611556|gb|CK039268.1|CK039268EST: AAGGATCCCAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAG GTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATG
genomic: AAGGATCCCAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAGgtattttata ... tttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATG
EST:
gi|29625686|gb|CB630697.1|CB630697EST: AAGGATCCCAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAG GTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATG
genomic: AAGGATCCCAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAGgtattttata ... tttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATG
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:
72 (upstream exon),
71 (downstream exon)
Score:
49GATGAAATTTGTTGGTACTGATGAGTTACCTGGGCCCGCACCAACTCAACAAGGATCCCAAATTGATCATTCTTTTCCTTTCCTAGAATCTCTAAATGAGgtattttata ... tttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtgccatatgaccatcatgggttctcatagaagttttttttgtttgttgcagGTCTTGGAAACTAATAGGGCTGAGGAATCGCATGGGCATGTACACAGGATGTATTTCATGGGCCCCAACACCTTCAGTGAACCTTGGCATCTCCCACACA
ttttttttgtttgtt CT-rich tract
atagaagtttttttt TA-rich tract