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mmu_ciR3hdm2_577
Basic information of circular RNA
PanCircBase ID:
mmu_ciR3hdm2_577
mm39_Chr. Position ID:
chr10|127294067|127294644|+
Gene name:
R3hdm2
Transcript:
ENSMUST00000166820.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
9
Exon/intron offsets:
0
Genomic length:
577
Exon/intron sizes in nt:
577
Flanking exon/introns:
chr10:127294067-127294678
Splice length:
577
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAGGTTTCTCTGATGAACTAAATGCACTTGGGAGGAAGTGGGGACAGCCTAGGGCATCAGTCTTTCCTCAAAGGAAGAATGTATGGAAGTAATTACTCCCTGGGAGAAAGAATTTGGGAGAGGGGCTGGAGAGATGGCTCAGAGGTTAAGAGCACCAACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACGTGGTGGCTCACAACCATCTGTAATGGGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCAACAGTGTACTCATTATATATATAAAATAAATGATTCTTTAAAAAAAAAAAAAAGACAGAGAAAGAAACAATCTTGAAAATTTAAACTTGAGCCAACAAGAGTTTATATTGTTTTTAGCAGCTAGGTTTTTGCCCCAGATATACTCTTCCCCCATTTTCCTTTAGCTGACAACATTCAGATGGGTGGAAGCGAGGCCTTAGGTAGCACCACGCAATGGGAACAAGCAGTGTTGCTAGGGGCTGGAACACATTCATGTACAAAATATGGTCTTCCACTACTAAGAAGAATTAGTTGGCTTCTGTTGTTGCTGTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGTTGCTAGGGGCTGGAAC
60.96
CTAGGCTGTCCCCACTTCCT
60.62
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAGGGGCTGGAACACATT
60.03
TGAGGAAAGACTGATGCCCT
58.34
153
PCR template sequence:
ATGGGAACAAGCAGTGTTGCTAGGGGCTGGAACACATTCATGTACAAAATATGGTCTTCCACTACTAAGAAGAATTAGTTGGCTTCTGTTGTTGCTGTCTGTAGGTTTCTCTGATGAACTAAATGCACTTGGGAGGAAGTGGGGACAGCCTAGGGCATCAGTCTTTCCTCAAAGGAAGAATGTATGGAAGTAATTACTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-7b-5p(1), mmu-miR-150-5p(1), mmu-miR-7a-5p(1), mmu-miR-326-3p(1), mmu-miR-1198-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTGTTGCTGTCTGTAGGTTTCTCTG
siRNA sets
AGAGAAACCTACAGACAGC, GAGAAACCTACAGACAGCA, CAGAGAAACCTACAGACAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIR3HDM2_577_ORF_3
0.6356
-0.287844621
0.026092836
228
ORF sequence:
ATGGGTGGAAGCGAGGCCTTAGGTAGCACCACGCAATGGGAACAAGCAGTGTTGCTAGGGGCTGGAACACATTCATGTACAAAATATGGTCTTCCACTACTAAGAAGAATTAGTTGGCTTCTGTTGTTGCTGTCTGTAGGTTTCTCTGATGAACTAAATGCACTTGGGAGGAAGTGGGGACAGCCTAGGGCATCAGTCTTTCCTCAAAGGAAGAATGTATGGAAGTAA
Peptide sequence:
MGGSEALGSTTQWEQAVLLGAGTHSCTKYGLPLLRRISWLLLLLSVGFSDELNALGRKWGQPRASVFPQRKNVWK
IRESfinder result
IRESfinder score
0.723184155
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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