Sequence
atgc intronic sequence ATGC exonic sequenceGTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgttgtggcctgattgcttttttgtcccctcagtaatatttgttgttaaagacagcaactaagtgataaccaatgtttcatgcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56580.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 6
GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgttgtggcctgattgctt--ttttgtcccctcagtaatatttgttgttaa---agacagcaactaagtga---taaccaatgtttca-tgcag-----
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GTCATGGACATGCTTGGGCCCAGTCTTTGGGATGTATGGAATTCTGTTGGTCAACAgtaagatttgtaccctcccttttgttagtataggttcacttttaatagctgcaatttatttaaactcttcctatataagccccattaacattttagttctggacag
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 6
GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgttgtggcctgattgcttttttgtcccctcagtaatatttgttgttaaagacagcaactaagtgataaccaatgtttcatgcag
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GTCATGGACATGCTTGGGCCTAGCCTTTGGGATGTTTGGAATTCTTTGGCTCAATCgtaag-------tacttttatca-ttctatattttcttaccaac-catgctcatgcagata-tgctaaatttattatttttctatttggtag
upper sequence: LOC_Os01g56580.2 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 6
GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgttgtggcctgattgcttttttgtcccctcagtaatatttgttgttaaagacagcaactaagtgataaccaatgtttc---atgcag------
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GTCATGGACATGTTGGGGCCAAGTCTTTGGGATCTTTGGAATTCTGTAGGCCAGACgtaagaa-atagaatctctctctctctctctctctcacacacacacacacacaagtggacattttttttcctgtttttaatttatttaaatcctgtaacagMapped 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|29629024|gb|CB634035.1|CB634035EST: GACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC GATGACCCCAAGTATGGTTGCTTGCATCGCTGTAGAGGCAATTTCTATCCT
genomic: GACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgt ... tttcatgcagGATGACCCCAAGTATGGTTGCTTGCATCGCTGTAGAGGCAATTTCTATCCT
EST:
gi|29623307|gb|CB628318.1|CB628318EST: GACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC GATGACCCCAAGTATGGTTGCTTGCATCGCTGTAGAGGCAATTTCTATCCT
genomic: GACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgt ... tttcatgcagGATGACCCCAAGTATGGTTGCTTGCATCGCTGTAGAGGCAATTTCTATCCT
EST:
gi|58661787|gb|CK050467.1|CK050467EST: GACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGAC GATGACCCCAAGTATGGTTGCTTGCATCGC
genomic: GACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgt ... tttcatgcagGATGACCCCAAGTATGGTTGCTTGCATCGC
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:
56 (upstream exon),
72 (downstream exon)
Score:
50GTAATGGACATACTAGGACCTAGTCTTTGGGATGTTTGGAATTCTGTTGGGCAGACgtaagattgt ... tttcatgcagGATGACCCCAAGTATGGTTGCTTGCATCGCTGTAGAGGCAATTTCTATCCTTGAGAAACTTCATGCAAAGGG
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