Sequence
atgc intronic sequence ATGC exonic sequencegcaaagctctgttcttctattgtaggattattaaaactattttgccagttgccttattagacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07070.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G151614_T03 (Zea mays), 3'ss of exon 10
gcaaagctctgttcttctattgtaggattattaaaactattttgccagttgccttatt-agacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
|||| | || ||| | ||| | | |||| |||||| | | ||||||||| || || ||||| ||||||||||||||||||||||||||||||| | |||||||||||||| |||||||||||||| || |||||||| ||||| ||||| |||||
gcaa-gttcagtttt---attctggatttatctgaactatgtattgtgctgccttatttagttgctgtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTAGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCATTAAAG
upper sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G173777_T01 (Zea mays), 3'ss of exon 9
gcaaagctctgttcttctattgtaggattattaaaac---tattttgcca-gttgccttattagacactag-cattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
|||| | | ||| |||| || || ||| | || | | | | | ||||||||| | | ||||| ||||||||||||||||||||||||||||||| |||||||||||||||| |||||||||||||| || |||||||| ||||| ||||| ||||||
gcaa-gttttgtgcttccatagtttcattctggaatcatgtgatatattgtgctgccttatttagttgtggtcatttgcagGTCCAACTCATGTTTTAGTTGTTCGTGGCTTGGATGAAAATGCTGATGAGGAAATGCTTCGGTACGAATTTGCTAAGCACGCACCAATAAAG
upper sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G35510.1 (Glycine max), 3'ss of exon 8
gcaaagctctgttcttctattgtaggattattaaaactattttgccagttgccttattagacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
||| || | || | ||| ||| | || | | | |||| | | ||||||||||||||||| | ||||| ||||| |||||||||||||||| ||||||||||| || ||||| ||| |||| ||||| || || |||
-gtaagtataactcctgtacc-tgacattg-----actttattaat-gctctgtaattaactatatgtgcaatcagGTCCAACTCATGTGCTTGTTGTCCGTGGATTGGATGAAAATGCTGATGAGGAAATGCTCCGCTATGAGTTTTCCAAACATGCTCCGATTAAG
upper sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G18030.1 (Glycine max), 3'ss of exon 8
gcaaagctctgttcttctattgtaggattattaaaactattttgccagttgccttattagacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
||| || || | ||| | || | || | | | |||| | | ||||||||||||||||| || ||||| ||||| ||||||||||||| || ||||||||||| || ||||| ||| |||| ||||| || || |||
-gtaagtataactcccgtacctga----cattgatgctttattaat-gctttgtaattaactatatgtgcaatcagGTCCAACTCATGTGTTGGTTGTCCGTGGATTGGATGAAAATGCGGATGAGGAAATGCTCCGCTATGAGTTTTCCAAACATGCTCCGATTAAG
upper sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT3G54230.2 (Arabidopsis thaliana), 3'ss of exon 10
-------------------------------------------------------------------gcaaagctctgttcttctattgtaggattattaaaactattt-tgcc--agttgccttattagacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
|| || | |||| |||| || | | | || | | || || | | || | | | | ||| |||||||||||||||| | ||||| ||||| |||||||| ||||||| |||||||||||||| ||||||||| |||| ||||| ||||| |||
gttctgatcagcatttttatttaagatgttttaaatttctttcttgagtcagaaacagtcgcaactgttaaggccatagtctt----tgtacttttctacatgccatatatacctaagatacatt-ctgcttattttcttttccagGTCCAACTCATGTCCTGGTTGTACGTGGGTTGGATGAAGATGCTGATGAGGAAATGCTTCGGTATGAATTTTCCAAACATGCTCCTATCAAG
upper sequence: LOC_Os02g07070.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 3'ss of exon 8
---gcaaagctctgttcttctattgtaggat-tattaaa-actattttgccagttgccttattagacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
| || ||| || | | | | || ||||| | ||| || || | | || || | |||||||| | |||||||| |||||||| ||| |||||||||||||||| |||||||||||||| ||||||||| | || ||||| || || |||
gttggaacactccattgcttttaattggcatgcattaagcattatattcattgtaatttgctaagttgata-tgtaatcagGTCCTATCCATGTTTTGGTTGTTCGAGGTTTGGATGAAAATGCTGATGAGGAAATGCTTCGTTATGAATTTTCTAAACATGCTCCAATCAAGMapped 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|33675774|gb|CF304013.1|CF304013EST: TGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAG GTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGG
genomic: TGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAGgcaaagctct ... gcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGG
EST:
gi|58611340|gb|CK039052.1|CK039052EST: TGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAG GTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGG
genomic: TGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAGgcaaagctct ... gcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGG
EST:
gi|29629290|gb|CB634301.1|CB634301EST: TGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAG GTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGG
genomic: TGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAGgcaaagctct ... gcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGG
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:
63 (upstream exon),
68 (downstream exon)
Score:
6TGTAATGAACCACGAACGGAAGATTCTCTACCAGCTGATCCAACAAGTTCTACTCCACTCCATCCAAAAAGGGGATCTGAACTAGgcaaagctct ... gcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaggattattaaaactattttgccagttgccttattagacactagcattttcagGTCCAACTCATGTTTTAGTTGTTCGTGGTCTGGATGAAAATGCTGACGAGGAAATGCTTCGATATGAATTTGCCAAGCATGCACCTATAAAG
cattttc CT-rich tract
attattaaaactattt TA-rich tract