Sequence
atgc intronic sequence ATGC exonic sequenceGCCCCCTCCGTGGCGGAGCGGATCGAACGCCTCATGAACCAAGCCGCCGGCGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattctttctgtcagtagaatttagcttccgcatgcgcgtaggcctgtcgtataacagctgcgcgtcaaaagctatggttttgttgggaattcgctag...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g46020.2 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g46020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G147614_T05 (Zea mays), 5'ss of exon 2
--GCCCCC-TCCGTGGCGGAGCGGATCGAACGCCTCATGAACCAAGCCGCCGGCGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattctttct-gtcagtagaatttagcttccgcatgcgcgtaggcctgtcgtataacagct-gcgcgtcaaaagctatggttttgttgggaattcgctag
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GTGCCGCCATCCGTCGCAGAGCGGATCGAGCGCCTCATGAATGAATCCGC---CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttacctcatttcccccgtctctcatcctcgaatcctaccccctttctccgaaaacctagcgtgtactaggcaagaagccccttcggaaaccgcg--
upper sequence: LOC_Os01g46020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G029038_T01 (Zea mays), 5'ss of exon 1
--GCCCCC-TCCGTGGCGGAGCGGATCGAACGCCTCATGAACCAAGCCGCCGGCGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattct-ttctgtcagtagaatttagcttccgcatgcgcgtaggcctgtcgtataacagctgcgcgtcaaaagctatggttttgttgggaattcgctag--
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GTGCCGCCATCCGCCGCAGAGCGGATCGAGCGCCTCATGAATGAATCTGC---CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttactttaccccatttcccccgtctctcatcctcgaatcc-taccccctttctccgaaaacctagcgt--gtggcaagaagccccttcggaaaccgcggttc
upper sequence: LOC_Os01g46020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G454830_T01 (Zea mays), 5'ss of exon 2
--GCCCCC-TCCGTGGCGGAGCGGATCGAACGCCTCATGAACCAAGCCGCCGGCGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattct-ttctgtcagtagaatttagcttccgcatgcgcgtaggcctgtcgtataacagctgcgcgtcaaaagctatggttttgttgggaattcgctag--
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GTGCCGCCATCCGTCGCAGAGTGGATCGAGCGCCTCATGAATGAATCTGT---TGCCTCCTCCTCCAACCCCGATGAGGCCTCCCTGGACCTCTCCTTCTTAGgttagtttaccccatttccctcgtctctcatcctcgaa-acctaccccctttctccgaaaacctagcgt--gtggcaagaatccccttcggaaaccgcagttc
upper sequence: LOC_Os01g46020.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G143935_T01 (Zea mays), 5'ss of exon 1
--GCCCCC-TCCGTGGCGGAGCGGATCGAACGCCTCATGAACCAAGCCGCCGGCGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattctttctgtcagtagaatttagcttccgcatgcgcgtaggcctgtcgtataacagctgcgcgtcaaaagctatggttttgttgggaattcgctag---
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GTGCCGCCATCCGTCGCAGAGCGGATCGAGCGCCTCATGAATGAATCCGC---CGCCTCCTCCTCCAACCCCCACGAGGCCTCCCTCGACCTCTCCTTCTCAGgttagtttaccccatttccccgtctctcatcctcgaatcc-taccccctttctccgaaaacctagcgt--gtggcaagaagccccttcggaaaccgcggttcaMapped 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|163929559|gb|EG713490.1|EG713490EST: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAG AGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
genomic: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
EST:
gi|88355167|gb|CI651870.1|CI651870EST: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAG AGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
genomic: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
EST:
gi|218499703|gb|FG961375.1|FG961375EST: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAG AGGATGGAAGAAGTGGCCCATTTAGGATTGGAAATGAAAGCTTTCCAGCAT
genomic: CGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCAT
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),
18 (downstream exon)
Score:
1GCCCCCTCCGTGGCGGAGCGGATCGAACGCCTCATGAACCAAGCCGCCGGCGCGTCATCCTCCAACCCCGACGACGCCTCCCTCGATCTCTCCTTCTCAGgtgattcttt ... cgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA
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