Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g31290.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 1
gtatgtgtaacaactgt-taatttaggttcattt--ttttttcttgcctttgccttct-tttctgtcattttcatgtatttctaattgact---tgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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---------------gtatgttttgagatcactcagttttatgctacatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 11
gtatgtgtaacaactgt-taatttaggttcattt--ttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgact---tgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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---------------gtatgttttgagatcaccaaattttatgctacatttatgttctgtctcaatatattcttttgtt-ctggttggttctttcgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGACTTTATTTACTTGCCAATTGATTTTAAG
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 3
-gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttg--ggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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agttttttctgaaaatgaagaattatgttcagttctacacctcatttacataattttttcttgaaacatctttt-tctgggactgatttgttgtcttgcagGTATACATCCAAGATGCTGTTAGCTGCAATTGATGAACGCCATAGAGGAACTTATGATTTTGTTTATCTGCCAATTGATTTCAGA
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggttt-agGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------------gtatgtgtaacaactgttaatttaggttcatttttt------tttcttgcctttgccttc--ttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggttt-agGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
gtatgtgtaacaact-gttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatt--tctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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-cattcatttctatttgtggttttacacaccataattgctcagattcctgttgcatcctctgttatttctgccttttgatttgatataatggtaattgtagGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA
upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatt--tctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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-----------------------------------------------tgttgcatcctctattatttctgccttttgatttgatataatggtaattataggtatacttcaaaaatgcttcttgctacaattgatgaacaccattgagGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAAMapped 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|58687890|gb|CK076577.1|CK076577EST: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
EST:
gi|58691922|gb|CK080609.1|CK080609EST: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
EST:
gi|56158059|gb|C72031.2|C72031EST: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
EST:
gi|66930475|gb|CX117323.1|CX117323EST: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
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),
74 (downstream exon)
Score:
123ATCAGTCTGATAATAAAAAGCAATATGAGCTTGATGTTGACCGCATTGTTCGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
attttcatgtattt TA-rich tract