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mmu_circSbno1_403
Basic information of circular RNA
PanCircBase ID:
mmu_circSbno1_403
mm39_Chr. Position ID:
chr5|124516532|124519840|-
Gene name:
Sbno1
Transcript:
ENSMUST00000065263.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
30,29,28,27
Exon/intron offsets:
0,815,3039,3213
Genomic length:
3308
Exon/intron sizes in nt:
77,138,93,95
Flanking exon/introns:
chr5:124514354-124516532|chr5:124519840-124519921
Splice length:
403
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATCTGGGTTCTGGAGATGAGAAGGTGAGGAAGAGTGATGTCAAGAAGTTTCTAACTCCAGGGTATTCAACCTCCGGCCATGTAGAGTTATACACGATTAGTGTGGAGAGGGGAATGTCCTGGGAGGAAGCAACCAAGATTTGGGCAGAGCTGACTGGACCAGATGATGGCTTTTACTTATCATTGCAGATAAGAAACAACAAAAAAACTGCAATCTTAGTTAAAGAAGTAAACCCTAAGAAGAAACTATTTTTAATTTACCGACCAAACACTGGGAAGCAACTCAAATTAGAAATTTATGCTGACCTGAAAAAGAAATATAAGAAGGTAGTTTCTGATGACGCCCTGGTACACTGGCTGGATCAGTATAACTCCTCTGCAGACACCTGTACTCACGCATACTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTTCTGATGACGCCCTGG
60.04
TCGTGTATAACTCTACATGGCCG
60
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCTGGTACACTGGCTGGATC
59.82
TCGTGTATAACTCTACATGGCCG
60
156
PCR template sequence:
ACCTGAAAAAGAAATATAAGAAGGTAGTTTCTGATGACGCCCTGGTACACTGGCTGGATCAGTATAACTCCTCTGCAGACACCTGTACTCACGCATACTGATCTGGGTTCTGGAGATGAGAAGGTGAGGAAGAGTGATGTCAAGAAGTTTCTAACTCCAGGGTATTCAACCTCCGGCCATGTAGAGTTATACACGATTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCACGCATACTGATCTGGGTTCTGG
siRNA sets
AACCCAGATCAGTATGCGT, AGAACCCAGATCAGTATGC, GAACCCAGATCAGTATGCG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSBNO1_403_ORF_1
0.875
0.116337135
0.554313914
468
ORF sequence:
ATGACGCCCTGGTACACTGGCTGGATCAGTATAACTCCTCTGCAGACACCTGTACTCACGCATACTGATCTGGGTTCTGGAGATGAGAAGGTGAGGAAGAGTGATGTCAAGAAGTTTCTAACTCCAGGGTATTCAACCTCCGGCCATGTAGAGTTATACACGATTAGTGTGGAGAGGGGAATGTCCTGGGAGGAAGCAACCAAGATTTGGGCAGAGCTGACTGGACCAGATGATGGCTTTTACTTATCATTGCAGATAAGAAACAACAAAAAAACTGCAATCTTAGTTAAAGAAGTAAACCCTAAGAAGAAACTATTTTTAATTTACCGACCAAACACTGGGAAGCAACTCAAATTAGAAATTTATGCTGACCTGAAAAAGAAATATAAGAAGGTAGTTTCTGATGACGCCCTGGTACACTGGCTGGATCAGTATAACTCCTCTGCAGACACCTGTACTCACGCATAC
Peptide sequence:
MTPWYTGWISITPLQTPVLTHTDLGSGDEKVRKSDVKKFLTPGYSTSGHVELYTISVERGMSWEEATKIWAELTGPDDGFYLSLQIRNNKKTAILVKEVNPKKKLFLIYRPNTGKQLKLEIYADLKKKYKKVVSDDALVHWLDQYNSSADTCTHAY
IRESfinder result
IRESfinder score
0.439902679
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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