Sequence
atgc intronic sequence ATGC exonic sequencegtgagtaacttgcaaagttgttgaatctccttcaatcttattggaaccacattttctaagagagtccattcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g15750.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 22
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgagtaacttgcaaagttgttgaatctccttcaatcttattgga--accacattttctaagagagtccat-----tcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA
|| ||| || | ||| |||||| || || || ||| ||| ||| ||| | | ||| | |||||||||||| | ||||| || ||||||| ||||||||||||||| | ||||| || |||||||||||||| |||| || |||| | |
gtaagttcattctttttgtcaccaatagaaccaaatcttttttgatagttggatgttcaaaggtttctcatgcggaccttatttatgcagAACCGCACTTGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAAACCAATCATACTCGGGAAGTACCATTATGTGCTGTACTTCCTCGTTTTG
upper sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 22
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgagtaacttgcaaagttgttgaatctccttcaatcttattggaaccacatt-----ttctaaga--gagtccattcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA
|| ||| | | || | | || | | ||| | | | | |||| || | |||| | || | || | || | |||||||||||| | ||||| | ||||||| |||||||||||||||||||| || |||||||| || || || |||| || |||||| |
gtaagtta-taacatatattttatgtatactttgctttcaa-agctccaccttgtgaatcctaaacttgggtgttgtattttgtacctagAACCGCACTTGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTG
upper sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 22
---------------gtgagtaacttgcaaagttgttgaatctccttcaatctta--ttggaaccacattttctaagagagtccattcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA
| || | | | | | |||| || || | || | ||||||||| | |||| | ||| || |||||||| | || || | |||||||| |||||||||||||| ||||||| ||||||| |||||||| | |||||| |||||| |
atataacaagagggtgcaagagatatctacaaacagccatcctccaacatgtctagcctcaaagcctattttctaaatcttgcttctcttttgcctacagATCTGCCCTTGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTGMapped 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|86592847|gb|CI270404.1|CI270404EST: CGGTTCCTTCTGTCCCC CATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAA
genomic: CGGTTCCTTCTGTCCCCgtgagtaact ... cacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAA
EST:
gi|8527826|gb|AU092641.1|AU092641EST: TCACTCTGACCCGGTTCCTTCTGTCCCC CATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCNTTGACATGAA
genomic: TCACTCTGA-CCGGTTCCTTCTGTCCCCgtgagtaact ... cacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAA
EST:
gi|29644400|gb|CB649407.1|CB649407EST: GGTTTGCTGACCCTTTCGCCATATCACTCTGACCGGTTCCTTCTGTCCCC CATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAA
genomic: GGTTTGCTGACCCTTTCGCCATATCACTCTGACCGGTTCCTTCTGTCCCCgtgagtaact ... cacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAA
EST:
gi|218478818|gb|FG953673.1|FG953673EST: GGTTTGCTGACCCTTTCGCCATATCACTCTGACCGGTTCCTTCTGTCCCC CATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGTCTTGACATGAA
genomic: GGTTTGCTGACCCTTTCGCCATATCACTCTGACCGGTTCCTTCTGTCCCCgtgagtaact ... cacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAA
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),
65 (downstream exon)
Score:
22GTGAGGATTGCTCAAGGTCTTGTTCACCTTGGGAAGGGTTTGCTGACCCTTTCGCCATATCACTCTGACCGGTTCCTTCTGTCCCCgtgagtaact ... cacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttcaatcttattggaaccacattttctaagagagtccattcttcacttttcagCATAGCACTTGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTA
tccattcttcactttt CT-rich tract
aatcttatt TA-rich tract