Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g19700.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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-------gtaagttaatgaataggattatgcagtgtgtgtctcattatttacatactgttgcatcttatgttatattgcttgtatagGAGTATAATGCAAAACTCTCCGATTTTGGGCTTGCAAAAGACGGACCTGTAGGTGATAAAACTCATGTCTCTACTCGAGTAATGGGAACCTATGGATATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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-------gtaagttaatgaataggattatgcagtgtgtgcttcatgatctatatactgctacatcatatgttatattgcttgtacagGAGTATAACGCAAAGCTCTCTGATTTTGGGCTTGCGAAAGACGGACCTGTAGGTGATAAAACTCATGTTTCTACTCGAGTAATGGGAACCTATGGATATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtaagtgtcaaaaactacaataagattgcat----------------ttcccccttttta--tcagtctaatattgtaccgattcagGAGTACAATGCCAAGCTCTCAGATTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G05260.1 (Glycine max), 3'ss of exon 3
---gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtaataacttgaatattgtttcattgcttactatgctaactttcaacagataaacacctttacctgcatcttaacatcattctgttttagGACTACAATGCAAAACTTTCTGACTTTGGGCTTGCGCAAGATGCTCCAGTGGGAGATAAAAGTCACGTTTCCACTGAAGTAATGGGAACACAAGGTTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgttttt--agGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtaagtgccaaatt-ttaaatt--attac-catttttcttttcat--tccttgatttg---atttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttg--taattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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-------gtaagtggccaaat--gttaagttattac-catctttcttttcattccttgatttgatctttatattattataacaattcagGAATACAATTCTAAGCTCTCAGATTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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---gtatgtaggtgaaggtatta-attatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaa---atgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtaagtgcccgaaactacaataagattgcatatttcctcct------------ttttgttagtcta-atattgccccaatt---cagGACTACAATGCCAAGCTCTCAGACTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGGGTGATGGGAACCTATGGTTACG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
-gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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ggtatgtgagttaaccaggaaaaaggtttttaattattttctatccatcctccaacataaaaacataaaaacataattgttttt--aGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G02730.1 (Glycine max), 3'ss of exon 3
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtaataacttgaatgttccattgcttactatactaactttcaacatataaacacctttacttacctcttaatatcattctattttagGACTACAATGCAAAACTTTCTGACTTTGGGCTTGCCCAAGATGCTCCAGTGGGAGATAAAACTCATGTTTCCACTGAAGTAATGGGAACACAAGGCTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttaagtccttgaattggattacgtattgcacaccacacgattcacatcttgtaattttgta--tattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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-----------gtacgtatctc---ttactctttaggatcaacat--cttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G01300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttaag--tccttgaatt---ggatta-cgtattgcacac-cacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtatgttttcctcttctttatatcaagggatcaacatcttatatacacgtctgtttctttgcttctaaagtcttac--catgtcccaatttcagGAGTACAATGCTAAATTATCAGATTTTGGGCTTGCCAAAGATGCTCCTGATGAAGGCAAAACTCATGTGTCTACTCGAGTCATGGGCACTTATGGTTACG
upper sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttttaagtcc-ttgaattggattacgt-attgcacaccacacgattcacatcttgtaatttt-gtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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gtatgtctgaaagccacttaacccgataacctcaactctgtcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATGMapped 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|3761134|gb|C98382.1|C98382EST: TGATTTTAAAACATCTAATATACTGCTAGATGCT GATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
genomic: TGATTTTAAAACATCTAATATACTGCTAGATGCTgtaagtttta ... actcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
EST:
gi|163929492|gb|EG709283.1|EG709283EST: GACCAGTTATTTACCGTGATTTTAAAACATCTAATATACTGCTAGATGCT GATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
genomic: GACCAGTTATTTACCGTGATTTTAAAACATCTAATATACTGCTAGATGCTgtaagtttta ... actcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTA
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),
75 (downstream exon)
Score:
29TGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTACCGTGATTTTAAAACATCTAATATACTGCTAGATGCTgtaagtttta ... actcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcacaccacacgattcacatcttgtaattttgtatattatgctactcttgcagGATTACAATGCAAAACTCTCAGATTTTGGGCTTGCCAAAGATGGCCCTGTAGGTGACAAAACTCACGTGTCTACTCGAGTAATGGGAACATATGGTTATG
ctactctt CT-rich tract
atcttgtaattttgta TA-rich tract