Sequence
atgc intronic sequence ATGC exonic sequencegtaagtacatgtgcatcaagaaggcttcctttcatgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62080.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
gtaagtacatgtgcatcaagaaggcttcctttca--tgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
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gtaagtgaatatgcgtcaagaaggctatactttacttgtttttgatgatcaggttatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT
upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 3
--------------gtaagtacatgtgcatcaag---aaggcttcctttcatgttttggatggtcagaatttaatattgaattac-taactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
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gtaagtatttattgatatttgtaatttgattaaatgaaggaatgtgcattatcatgcgagttgaaaaacttgtggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAATTATCGTTCTTTATCAATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT
upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 5
-----------------------------gtaagt-acatgtgcatcaaga-aggcttcctttcatgttttggatggtcagaa-tttaatattgaatt--actaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
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gtaagtatttattgatatttgtaatttaattaaatgacaggaatgtctattcaatcatgcttaaatattctgtgagttaaaaaacttgcggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTATCGTTCTTTTCCTATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT
upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------gtaagtacatgtgcatcaagaaggcttcct---ttcatgttttggatggtc----agaatttaatattgaatt--actaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
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gtaagtgctgttacctttatttgacaagtttgaggggaaaatgcaatttcttcacgcccaaatgttatgtgagttaaaagaacttgcgcatgggtttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTACCGTTCATTTCCCATTGATCTTGTTCGGGAGCTTGGCAGACAACTTTMapped 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|117243444|gb|CT848361.1|CT848361EST: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST:
gi|58654607|gb|CK043287.1|CK043287EST: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST:
gi|29665089|gb|CB661364.1|CB661364EST: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST:
gi|29679261|gb|CB675536.1|CB675536EST: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
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:
75 (upstream exon),
72 (downstream exon)
Score:
42CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctttcatgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
tactaac putative branch site (score: 42)
ctttgtc CT-rich tract
agaatttaatattgaa TA-rich tract