Sequence
atgc intronic sequence ATGC exonic sequencegtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g43350.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G072865_T01 (Zea mays), 3'ss of exon 10
gtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
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gtttgaacttaagcaattactgatagaacaatctgataaaaaag--gatctaatttggctttttaatgttgaattt------aacagAAATTGAGTATATTGCCAAGATCTGGAGGTGCATTAGGCTTCACGTACACCCCTCCCGTCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G163193_T03 (Zea mays), 3'ss of exon 9
gtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
|||||||| |||||| || ||||||||| | | ||| || | ||| | ||| | || || || | ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| ||||
gtttgaacttaagcaattactgatagaacaatctgagagaagatgtaatttgacttactttttcaatgctgaattt------aacagAAATTGAGTATATTGCCAAGGTCAGGAGGTGCATTAGGCTTTACATACACCCCTCCCACCACAGAGGATAGATATTTACTCTTTGTTGATGAACTACGTG
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G07280.1 (Glycine max), 3'ss of exon 10
--------gtttgaacgcaagcaactatcgatagaacagtttaag------aaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
||| | | | || | | | ||| | || || | || || | ||| | | ||| | ||| || |||||| | |||||||||||||||||||| || || ||||||||||| || | ||||| ||||| || |||||||| ||||| ||||| ||||| ||| ||
gtatataagttgtatcttggaaatctctatgttgcacatcattagtccttaaatactttaaggatgattcaatgccttaatat-gttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA0028S00210.1 (Glycine max), 3'ss of exon 10
--------gtttgaacgcaagcaactatcgatagaacagtttaag------aaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
||| | | | || | | | ||| | | || || | || || ||| | | || | ||| || |||||| | |||||||||||||||||||| || || ||||||||||| || | ||||| ||||| || |||||||| ||||| ||||| ||||| ||| ||
gtatataagttgtatcttggaaatctctatgttgcacattattagtccttaaatactttaaggatgattcagtgccttaatatc-ttgtgtttgtcatcagAAACTAAGTATATTGCCAAGGTCAGGAGGGGCTTTGGGCTTTACTTATATTCCTCCAACAACTGAGGATAGATACTTGCTATTTGTCGATGAGTTGCATG
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G58870.1 (Arabidopsis thaliana), 3'ss of exon 10
gtttgaacgcaagcaactatcgatagaacagtttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
| | || | | || | || | || || | || | | | | | | | || | ||||||| || ||||| ||||| ||||| || ||||||||||||||||||| || || || ||||| ||||||||||||||| |||||||||| | ||
----gtaaagcagtgagaaccg-catgttgcttgatactcattttttacatgtgttaatgctctgctaatacatattgtatttttagAAATTAAGCATATTACCAAGATCAGGAGGGGCATTGGGCTTTACATACATTCCCCCAACGCATGAAGACAGATATTTGCTCTTTATTGATGAACTACATG
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G47060.1 (Arabidopsis thaliana), 3'ss of exon 10
gtttgaacgcaagcaact-atcgatagaacagtttaa-gaaaatgttcgtcttgggcttaca-----ttttagtgttgttctttttt------ccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
| || |||| | | || | | | | | | ||||| || | | | | || || ||| ||| || | ||| |||||||| || ||||||||||| |||| || |||||||| |||||||||| ||||| || | ||||| |||||||| ||||| ||||||| |||| ||
-gtaaaatgcaaaaactttgtctacatttacgctcattgtttatgtt-gtttagtacgtgcaaatgattcaagttttgctcatctttgtggtgttgtcagAAATTAAGCATATTGCCAAGAACAGGAGGGGCATTGGGATTTACATACATTCCTCCTACTAGTGAAGACAGATATTTACTCTTCATTGATGAGCTGCTTG
upper sequence: LOC_Os02g43350.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv06s0004g06120.t01 (Vitis vinifera), 3'ss of exon 10
-gtttgaacgcaag-caactatcgataga-acagtttaaga----aaatgttcgtcttgggcttacat--tttagtgttgttcttttttc----caccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
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tactaggatgtgagtccatcacatgcatacatgctttgtcattttaaatcgtccgcgtaacattagatggtccaatgctatctgtattttgtgttcacagAAGTTGAGCATATTGCCAAGATCAGGAGGGGCATTGGGTTTTACATATACTCCTCCCACCAATGAGGACAGATATTTGCTGTTCATTGATGAGTTACGTGMapped 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|29687896|gb|CB684171.1|CB684171EST: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAG AAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACC
genomic: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgc ... tttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACC
EST:
gi|58695544|gb|CK084231.1|CK084231EST: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAG AAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACGTACACC
genomic: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgc ... tttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACC
EST:
gi|2799377|gb|AA752366.1|AA752366EST: TTGTGGGAACTGCTGTACCAAACCTATTGCCAGGGCAGCCACGTGTGGAG AAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACC
genomic: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgc ... tttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACC
EST:
gi|29674691|gb|CB670966.1|CB670966EST: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAG AAATTGAGTATATTGC
genomic: TTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgc ... tttccaccagAAATTGAGTATATTGC
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:
74 (upstream exon),
55 (downstream exon)
Score:
19GAAGGGTAATGAAAAGGCTGTTGTTGCACGGCATGAAGTTGGTCATGCCGTTGTGGGAACTGCTGTAGCAAACCTATTGCCAGGGCAGCCACGTGTGGAGgtttgaacgc ... tttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagaaaatgttcgtcttgggcttacattttagtgttgttcttttttccaccagAAATTGAGTATATTGCCAAGGTCAGGTGGTGCATTGGGCTTTACATACACCCCTCCCACAACAGAAGATAGATATTTGCTCTTTGTTGATGAACTGCGTG
ggcttac putative branch site (score: 19)
ttgttcttttttccac putative PPT
ttacatttta TA-rich tract