Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtttgccctcctatgattataaaataacctatcaaaattgccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g10940.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 5
----gtgtgtttgccctc--ctatgattataaaataacctatcaaaattgccatggccttacttc-tgtaaatt----------acttgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
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gtgagaattatagctataggctacaacttactggttatatgt-gacatacccttggcgttatttaatatgaagtctaattttgaatctacatgtacaaaatcgtgtaattctgggttatgatcattttacttaatgcagATATTTCGCAAGGAACCTTTTTTTTATGGTCACGACAACCATGATCAGCTTGTCAAAATAGCTAAG
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G05340.2 (Glycine max), 3'ss of exon 5
---------gtgtgtttgccctcctatgattataaaataacctatcaaaatt---gccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttatttactgt-ttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
| | | | || |||| | || | | ||| || | || | || | ||| || || | | | | || || ||| || ||| | | || ||||||||||||| ||||| ||||| ||||| || || |||||||| ||||||||||||||||| |||
gtgtgaattataactataagttactggttatatatggcatactcttgacatttatgcagatggtctaaatttg-agcgtacatgattaaaaatgtaaaattctggtcataatttgttcgttgtactcttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G22250.1 (Glycine max), 3'ss of exon 5
---------------gtgtgtt-tgccctcctatgattataaaataacctatcaaaattgccatggccttacttctgtaaattact-tgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
| | | | | || ||| | | || | ||| || | | ||| | | | | | | || ||| || | | | ||| | | | || ||| ||||||||||||||||||| ||||| ||||| ||||| |||||||||||||||||||||||||| |||
gtgagaattatagctataggctacaacttactggttatatgtgacatgctcttggcattatt-tgatatgaagtctaattttgaatctacatgtacaaa-atcgtgtaattctgggtttgatcatcttacttcatgtagATATTTCGCAAGGAACCTTTCTTTTATGGTCACGACAACCATGACCAGCTTGTCAAAATAGCTAAG
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 5
-------gtgtgtttgccctcctatgattataaa--ataacctatcaaaattgccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
| | | | |||||||| | | || | | ||| | || | | | | || ||| | | | || | ||| || || ||||||||||||| ||||| ||||| ||||| || || |||||||| ||||||||||||||||| |||
gtgtgaatcataactacaagtttctgattatatatggcatactcttgacatttatgcagatggtctaaatttgagcatacatgattaaaaatgtgagattctggtcataattttcattgtactttttgtagATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAG
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgtttgccctcctatgattataa-aataacctatcaaaattgccatggccttacttctgtaaatt--acttg-cgtatagaaagatagcaactgtta--tgctttattta--ctgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
| ||| | | | |||| | | | || | || |||| ||| | ||| | | || | |||| | | | || || | | |||| ||||| ||||||||||| |||||||| ||||| || ||||| |||||||||||||| ||||| ||||||
-------------gtaacagttacagtggcagttggtgttaattttcttttacatattacttgaaatgcagtttgtcttatcaataaat-gtaactttcaactactcaatggaggtttttttcccaacagATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAG
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgtttgccctcctatgattataaaataacctatcaaaattgccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttat-ttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
||| | || || ||| || || | | || || | | || | || | | | | | | ||| | ||| | || || || ||| |||| |||||||||||||||||||| ||||| || || || ||||| ||||||||||| || ||||||
gtgagatt-tactactactgttgatcttgaatcatttgaagggctgattgtgccatttacattttttgtatttattttaattatcattttgttttactcagtatacttctattatttatgtagATCTTTCGCAAGGAACCATTCTTTTATGGTCATGACAATCATGATCAGCTTGTCAAGATTGCCAAG
upper sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ20478 (Selaginella moellendorffii), 3'ss of exon 5
gtgtgtttgccctcctatgattataaaataacctatcaaaattgccatggccttacttctgtaaattacttgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
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------------------------------------------------------------gtgagtcttttgtct---gatcattcgtacttgcta------acgccccaagcttca--cagATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGMapped 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|87016659|gb|CI275661.1|CI275661EST: ATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
genomic: ATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATGgtgtgtttgc ... tttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
EST:
gi|66923472|gb|CX110320.1|CX110320EST: ATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
genomic: ATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATGgtgtgtttgc ... tttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
EST:
gi|25806912|gb|CA762873.1|CA762873EST: ATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
genomic: ATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATGgtgtgtttgc ... tttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
EST:
gi|86261473|gb|CI017215.1|CI017215EST: TATGTTTGCTGGAATG ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
genomic: TATGTTTGCTGGAATGgtgtgtttgc ... tttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTT
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:
66 (upstream exon),
65 (downstream exon)
Score:
15ATACTTCAAAGGGCCTGAATTGCTGGTTGACTTCCAAAGTTATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATGgtgtgtttgc ... tttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttgcgtatagaaagatagcaactgttatgctttatttactgtttttgatgcagATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG
ttttgat putative branch site (score: 15)
ctgttttt CT-rich tract
tttatttactgttttt TA-rich tract