Sequence
atgc intronic sequence ATGC exonic sequenceTTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaagtttatgtccttgaagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g38530.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G039811_T01 (Zea mays), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatatt-------ttgaagtttatgtccttgaagtaatatgc--cttaatctctgtttgccatcattctttttgtttgagctacag
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TTACTCCCTTCCATTCTGCAAGCCAGATGCCATAGTTGACAGTGCCGAAAATCTCGGGGAGGTTCTTCGTGGCGATCGCATTGAGAACTCTCCTTATGTGgttagtaccatatataacataacagattaattgaggttt-cgtcctcgggtaagtgtgtggcgtaatttttttctttc----tgattgttatttggggtatag
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G006117_T02 (Zea mays), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcata------ttttgaagtttatgtccttgaagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag
||| |||||||| |||||||||||||| || || || |||||||| |||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||| ||| || |||| | | || || |||||| | | || | | | | ||| |||| | ||| || |||| || ||
TTATTCCCTTCCGTTCTGCAAGCCAGATACCATAGTCGACAGTGCCGAAAATCTTGGGGAGGTACTTCGTGGCGATCGCATTGAGAACTCTCCTTATGTGgttagttccgtatataacataacagattaattgagattttgtcctcgggtatgtgtg---tgacatattttttccattctgcttgttatttggagtatag
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA06G06460.1 (Glycine max), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaagtttatgtccttgaagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag---------
||| || ||||| | ||| ||| || || || ||||| |||||||| || || || ||||||||||| ||||||||||| |||| |||||||| ||| | | | | || |||||| | ||| | ||| || | ||| || ||| |||| || |||
TTATTCACTTCCCTACTGTGCCCCATCAAAAATACAGGATAGTGCAGAAAATCTTGGGGAAGTACTTCGTGGTGACCGCATTGAGAATTCTCTCTATGTGgtcagt-cttacttgtttactcttgtcagttta-atttttgtggcaatgacaagaaaggaattcttgatgatatattttcagttt-aggaacaattaactgct
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G36550.1 (Glycine max), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagt--accgggtaactcatat---tttgaagtttatgtccttgaagtaatatgccttaatctctgtttgccatcattcttt--ttgtttgagctacag
|| || || |||| ||| |||| || || | |||||||| ||||| || || || ||||| || || ||||||||||| |||||||| ||||||||| || | | || | || || ||| | | || |||| | | | | | | || || || ||
CTATTCACTGCCTTATTGCCGGCCAAAACACATTTTCGACAGTGCAGAAAACCTGGGGGAAGTTCTCCGGGGAGATCGCATTGAAAACTCTCCCTATGTGgttggtttattaaatctttcggacaggttccaactttccaccttatgtttagtatgtttcactactaaaatattgaaacttttaaatttttccag------
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G34020.1 (Glycine max), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaagtttatgtccttgaa-gtaatatgcc--ttaatctctgtttgccatcattctttttgtttgagctacag
||| || ||||||| || ||| | | || || || |||||||||||||| || || || |||||||||||||||||||| || |||| |||||||| || | | ||||| | || ||| || | | ||||| | || | | | | ||| | |
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaa----attttaattcttgtgttgttaattatgttatgctaatcaacttatttgctctgacatatatgcag------------
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G11780.1 (Glycine max), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaagtttatgtccttgaagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag
||| || ||||||| || ||| | | || || || |||||||||||||| || || || |||||||||||||||||||| || |||| |||||||| || | | ||||| | || | || | |||| | | | | || | || || | | |||
TTATTCTCTTCCTTATTGTCCACCAAATAAAATAGTGGATAGTGCTGAAAATCTTGGAGAAGTGCTTCGTGGTGATCGCATTGAAAATTCTCGTTATGTGgtatgttttatatgaa----attttaattcttgccttgtta----attatgttatggttaccaact--tatt-tactcagtgacgtatttgcag
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G24170.1 (Arabidopsis thaliana), 5'ss of exon 3
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaagtttatgt-ccttg---aagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag
||| || ||||||| || |||||| ||| ||||| |||||||| ||||||||||| ||||||||||||||||| |||||||||||||| | |||||| || | | | || | || | ||| | |||| |||| || || | | | ||| || | | ||| ||| | | |||
TTATTCTCTTCCTTATTGTCGTCCAGAACATATTGTTGATAGTGCTGAGAATCTCGGTGAAGTTCTTCGTGGTGATCGAATTGAGAACTCTCCTTTTGTGgtatgttcttgtttcttcttggttctttctctatctgtcttggttaagtggtagttgttgagttgtttttaatgtctgtttgtttcttt--gttgcag
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttgaag-------tttatgtccttgaagtaatatgcc-ttaatctctgtttgccatcattctttttgtttgagctacag
|| || ||||||| ||| |||||||| || ||||||||||| || ||||| ||||| |||||||| |||||||| ||||| |||||||| |||||||| || | || | ||| ||| | ||||| ||||| | ||||| || || | | | || | || |||||| ||
CTATTCTCTTCCTTATTGCCGTCCAGAAACCATAGTTGACAGTGCAGAGAATCTTGGTGAAGTTCTTCGGGGTGATCGTATTGAAAACTCTCCTTATGTGgtctgt-tagagttcttaatactttagtgatcctcctttatatccttttcctg-tatgcagtttattagtttctaacag-aagctgtttgttgcag------
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcatattttga--agtttatgtccttgaagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag
|| || || |||| ||| |||| || || || |||| ||| || |||||||| || || |||||||||||||| ||||| ||||| || |||||||| ||| | | |||||| |||| | | | | || | | | | || ||| | | | |||||| ||
CTATTCTCTGCCTTATTGCCGCCCAGGAAAAATTGTGGACAATGCAGAGAATCTCGGGGAAGTGCTTCGTGGTGATCGTATTGAAAACTCCCCTTATGTGgtcagttttaacatcttgcttttttgacaagttgagggctgcttgtttatgttaataattgactcttttagctgagtggatttgttgcag------
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S140_64V6.1 (Physcomitrella patens), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGA---AACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggtaactcata-ttttgaagtttatg--tccttgaagtaatatgcct-taatctctgtttgccatcattctttttgtttgagctacag--
||| ||| | |||||||||| | || || ||||||| || || | || ||||||||||| |||||||||||||||||||| || || || || ||| | | || | | ||| | || || || || ||| | | || | || | | || | |||| | ||||
---CTCGCTTGACTACTGCAAGCCAAGTTCAGGGATTGTGAACAGTGCCGAGAACTTGGGAGAGGTTCTTCGAGGTGATCGCATTGAGAACTCACCTTACGTTgtacgtaatctctgagccaaagtcttggtgcacataattcttttcagcaatgttagtataccccttgagttgaaggctttatattgtacgttatacatct
upper sequence: LOC_Os09g38530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ35060 (Selaginella moellendorffii), 5'ss of exon 2
TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccgggta-actcatattttgaagtttatgtccttgaagtaatatgccttaatctctgtttgccatcattctttttgtttgagctacag
|| ||| | | || |||||||| | | || | |||| ||||| ||||| || ||||||||||| || |||||||| ||||| ||||| |||||||| ||| | | || || | | ||| || | | | |||| |
CTATTCCTTGGCATTTTGCAAGCCGGGGAAGGTCCTCAACAGCGCTGAGAATCTGGGCGAGGTTCTTCGAGGAGATCGCATCGAGAATTCTCCTTATGTGgtgagtttcatctctacctttagccaagggagaaaaaaagaaaagaaaaaggatgctaatgctgtggtgtag-----------------------Mapped 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|29627738|gb|CB632749.1|CB632749EST: ATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTG TTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTT
genomic: ATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccg ... tgagctacagTTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTT
EST:
gi|29627699|gb|CB632710.1|CB632710EST: ATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTG TTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTT
genomic: ATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccg ... tgagctacagTTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTT
EST:
gi|29630499|gb|CB635508.1|CB635508EST: ATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTG TTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTT
genomic: ATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccg ... tgagctacagTTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTT
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:
70 (upstream exon),
68 (downstream exon)
Score:
31TTACTCCCTTCCTTTCTGCAAGCCAGAAACTATCGTTGACAGTGCTGAAAATCTCGGTGAGGTTCTTCGTGGTGATCGCATTGAGAACTCTCCATATGTGgttagtaccg ... tgagctacagTTTCAAATGAGAGAGCCCAAGATGTGCCAGATTGTCTGCAAATTAACTGTTGGTGAGAAAGAAGCAAAGGAGCTCAAGGAAAAGATAGAGGATGAATATC
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