Sequence
atgc intronic sequence ATGC exonic sequenceGAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g27040.1 |
intron # | 22 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 22
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcag-------------------------
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GAAGAAGTTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAATATGGCCAAAATAAAGGGAAGTTCTATAATGAGGAATGTGACCGCTTTATGgtatgttccctc--accatattatgttt---atctatgtgagtacatgttatgtctactaagctgggtgtcacattccagctttgcatggtgcacaaacttggat
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 14
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttg---tcacatttcag
||||||| |||||||||| ||||| |||||||||||||||||||| ||||| || || || ||||||||||||||||| |||||||| ||||| ||||||||||| | | || ||||| | | | || | || | ||| || ||||||| ||| | || || | ||||| |||
GAAGAAGCTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAGTACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatgtttt-tctcaccatgtta---tgtgtatttatgtatttgagtacatgacatggctactaagctggagttacattccag
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 22
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatg----ctctatcataccatctcacttt-ctgcacacatttgttttca--aacgtgacat--gtct---aattagttgtcaca---tttcag
|||||||| |||||||| |||||||| ||| |||||||||| || |||||||| || |||||||||||||| || ||||| ||||| ||| | || |||||| | | || | | || | ||| || | | | | || | | | || || | || | ||| | | || |||
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAATGAAGAATGTGACAGATTCATGgtacaaattttatgtctttcaattttttttttctttctaggtctagctccatcatccttctatcggtttctaaaaaaattgctataaatttacag
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcag
|||||||| |||||||| |||||||| ||| |||||||||| || |||||||| || |||||||||||||| || || || ||||| ||| | || |||||| | | | | | | || || ||| ||| | | | || | | | | | || |||
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctc------catcatccttctatgggtttctaaaaaaattgctataaatttacag
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA07G38050.1 (Glycine max), 5'ss of exon 22
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatg----ctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcag--------------------------------------------------
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GAAGAAGTTGGACCGCTACAAGAATCCTTGGCTTGAATTGAAGATACAATATGGACAAAACAAAGGGAAGTTATACAATGAAGAATGTGACCGATTCATGgtgtgaaatttatttccttttgtttttatttttgcccaaatttatttcttttcgtt-catgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttttctgacttcacttaaaacttgcag
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgc------tctatcataccatctc-----actttctgcacacatttgttttcaaacgtgacat--gtctaattagttgtcacatttcag
|||||| | || ||||| | || || ||| | || |||| || || ||||| ||||||||||||||| | || ||||| || ||||||||||| |||||||| | ||||| || | | | || | | || | ||| || ||| || | || | | | ||||
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcag
upper sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 22
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctctatcataccatctc--actttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcag-----------------------
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GAAGAAGTTGGATCGCTACAAGAATCCATGGCTGGAACTAAAGATCCAGTATGGGCAAAACAAAGGGAAGTTGTACAATGAAGAATGCGATCGTTTTATGgtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtagMapped 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|58682000|gb|CK070687.1|CK070687EST: ATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGAGCGTTTTATG CTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCT
genomic: ATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctcta ... cacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCT
EST:
gi|84117441|gb|CD151208.1|CD151208EST: ATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATG CTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGGAAGCT
genomic: ATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctcta ... cacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCT
EST:
gi|396941444|gb|HO188653.1|HO188653EST: ATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATG CTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCT
genomic: ATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctcta ... cacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCT
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:
69 (upstream exon),
67 (downstream exon)
Score:
17GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctcta ... cacatttcagCTTTGCATGGTGCATAAGCTTGGTTATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGCATGTCGCCTTTGTTCCGATTTGATTGGTTTGTCAAGTCCA
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