Sequence
atgc intronic sequence ATGC exonic sequencegttcaatccccctcttccccttctcgccattgctctgcaacaatgcgcgcagcaagctgatgcgtgtcgatgaatctgagcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
Basic information
species | Oryza sativa |
transcript | LOC_Os09g36740.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G050268_T01 (Zea mays), 3'ss of exon 2
-----------------------gttcaatccccctcttccccttctcgc-cattgctctgcaacaatgcgcgcagcaagctgatgcgtgtcgatgaatc--tgagcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
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gttcgtgctcgtccttcgtctaccttttgtgcacgtatgtgtgttaacattcatgcctctgagacggtattaaatttaaatgcgctcttgctgctgtcttgatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGTTGCAGCGGATCCACCAGGGCCACGCCTTCAATGGCAAGCGGACCAAAACGGCTC
upper sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G000825_T01 (Zea mays), 3'ss of exon 2
gttcaatccccctcttccccttctcgccattgctctgcaa-------caatgcgcgcagcaagctgatgcgtgtcgatgaatctga----gcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
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gttcgtgctcgtacttcgtctac-cttaatttctctgcacgtgcgctcgattcatgcctctggctctgagacggtattaaatttaaatgcgcagAGATGCGGGCGGCTGGACGACCAAATCTCGCTGCTCAAGCACAAGCTGCAGCTGATCAACCAGGGCCACGCCTTCAACGGCAAGCGGACCAAAACGGCTC
upper sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ30150 (Selaginella moellendorffii), 3'ss of exon 2
gttcaatccccctcttccccttctcgccattgctctgcaacaatgcgcgcagcaagctgatgcgtgtcgatgaatctgagc-agAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
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-gtaagccccctttttcccccaaatccagtctctcggacatgtatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGC
upper sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ08332 (Selaginella moellendorffii), 3'ss of exon 2
gttcaatccccctcttccccttctcgccattgctctgcaacaatgcgcgcagcaagctgatgcgtgtcgatgaatctgagc-agAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
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-gtaagccccctttttcccccaaatccagtctctcggacatggatcgatgaaatcgctgacttgggcgattctctctctcccagAGGTGTGGCCGGCTGGACGATCAGATCGCTCTCCTCAAGCACAAGCTCCAGCTGATCTACGCGGGCCTCGCCTTCAATGGCAAGCGGACCAAGACCGCGCMapped 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|58676862|gb|CK065549.1|CK065549EST: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGACCTCTACAAG AGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGACCTCTACAAGgttcaatccc ... atctgagcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAG
EST:
gi|58671270|gb|CK059956.1|CK059956EST: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGACCTCTACAAG AGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAG
genomic: CCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGACCTCTACAAGgttcaatccc ... atctgagcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAG
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:
39 (upstream exon),
60 (downstream exon)
Score:
4CCGCGCGGAGGAGGCCATCGAGGCCATCAAGTCGCTGCGAAGCCGCTGCTCCGACCAGGCGCAGGAGTCCCTCGACAACATCCTCCTCGACCTCTACAAGgttcaatccc ... atctgagcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgctctgcaacaatgcgcgcagcaagctgatgcgtgtcgatgaatctgagcagAGATGCGGGCGGCTGGACGACCAGATCTCGCTGCTCAAGCACAAGCTGCAGCTCATCCACCAGGGCCACGCCTTCAACGGCAAGCGCACCAAGACGGCGC
agctgat putative branch site (score: 4)