Sequence
atgc intronic sequence ATGC exonic sequenceAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40590.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G028037_T02 (Zea mays), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCGgtaagcaactatattgaa----------atgttaaaaatattcattcatacaaatgtatt-------tgctaacatattt-ttttcag
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATATAGGGATTTTAAAACTTCAAACATATTACTGGATGCAgtaagtg-------tcaaaaactacaataagattgcatttccccctt----tttatcagtctaatatt--gtaccgattcag------
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCACTTGGTGCTGCAAAAGGTCTTACTTTTCTCCATGAAGAAGCTCAGAGGCCTGTAATCTATCGTGATTTTAAGACATCTAATATTCTGTTAGATGCGgtatgtgagttaaccaggaaa--aaggtttttaattattttttatccatcctccaacataaaaacataaaa-acataattgtttttag
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATATAGGGATTTTAAAACTTCAAACATATTACTAGATGCAgtaag------tgcccgaaactacaataagattgcatatttcctcct---ttttgttagtctaatattgccccaat--tcag------
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G49060.1 (Glycine max), 5'ss of exon 4
-AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TTGCACTTGGTGCTGCAAAAGGTCTTGCTTTTCTCCATGAAGAAGCTCAAAGACCTGTAATCTATCGTGATTTTAAGACGTCTAATATTCTATTAGATGCggtatgtgagttaaccaggaaa--aaggtttttaattattttctatccatcctccaacataaaaacataaaa-acataattgttttta-
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G02360.1 (Glycine max), 5'ss of exon 3
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCACTTGGTGCAGCCAAAGGTCTTGCTTTTCTCCATGAAGAGGCTCAGAGGCCCATAATATATCGTGATTTCAAAACATCTAATATACTATTAGATGCGgtatgtaggtgaaggtattaattatttcttatt--catcctccaaccaaaaagcaaaaatctaaaaaaac--aaatgtttatag----
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttct-taaatattcattttcag
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TGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATATAGGGATTTCAAAACTTCCAATATACTATTGGATGCAgtaagtggccaaatgttaagttattaccatctttcttttcattccttgatttg----atctttatattattataacaattcag------
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 5'ss of exon 5
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttct-taaatattcattttcag
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TGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATATAGGGATTTCAAAACTTCCAATATACTATTGGATGCAgtaagtg-ccaaattttaaattattaccatttttcttttcattccttgatttg----atttatatattattataactattcag------
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag-----
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TGCACTTGGTGCAGCTAAAGGTCTCGCCTTTCTTCACGAAGAAGCTGAGAAGCCAGTCATATATCGAGATTTCAAAACATCTAATATTTTACTGGATGGGgtatgtctgaaagccacttaacccgataacctcaactctgtcctttc---tctctatgtttataaattttagaaaaaaatgctcccattgcag
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATATCGTGATTTTAAGACCTCCAACATCCTATTGGATGCAgtaagtaa-------taaaaactgtgataaattc---acgtttgtctcc-taatatcattccatcttttatatgacatcctatttcag
upper sequence: LOC_Os01g40590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv14s0108g00380.t01 (Vitis vinifera), 5'ss of exon 4
AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcag
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TGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATATCGAGATTTTAAAACATCTAATATCCTGTTAGATGTGgtaggtgac-----ttaaaatgctttgcaaat-agtagtcctaacttatcct-tgtcttatttcaatttgtgaaacttgttcttccagMapped 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|218487386|gb|FG962477.1|FG962477EST: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCG GACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
genomic: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
EST:
gi|58599882|gb|CK010410.1|CK010410EST: GGCCAG-TATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCG GACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
genomic: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
EST:
gi|38480620|gb|CF964709.1|CF964709EST: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCG GACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
genomic: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
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:
70 (upstream exon),
74 (downstream exon)
Score:
7AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
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