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mmu_circHfm1_981
Basic information of circular RNA
PanCircBase ID:
mmu_circHfm1_981
mm39_Chr. Position ID:
chr5|107026456|107043207|-
Gene name:
Hfm1
Transcript:
ENSMUST00000117588.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
25,24,23,22,21,20,19,18,17,16
Exon/intron offsets:
0,212,1708,1844,3202,7920,11311,14107,14859,16605
Genomic length:
16751
Exon/intron sizes in nt:
1,32,98,48,10,79,28,14,00,00,00,000
Flanking exon/introns:
chr5:107022794-107026456|chr5:107043207-107043809
Splice length:
981
Other database IDs:
circBase: mmu_circ_0011963, CIRCpedia: MMU_CIRCpedia_213940, circAtlas: mmu-Hfm1_0008
Human Ortholog IDs:
Mature spliced Sequence:
TCACTACCAGTACTCTAGCTATGGGCATGAACATGCCGGCTCACCTGGTTGTTATAAAGTCTACCATGCACTACAGTGGAGGTGTGTTTGAAGAGTACAGCGAGACCGACATCCTGCAGATGATTGGGAGAGCTGGCAGACCCCAGTTTGACACTACAGCTACTGCAGTCATTATGACTCGACTAAGTACAAGAGAGAAGTACGTGCAGATGCTAGCTTGTAACGACACTGTAGAGAGCAGTTTGCACAGACATCTTATTGAACATTTAAATGCAGAAATAGTGCTGCATACCATCACAGACGTGAACATTGCTCTGGACTGGATCCGATCAACAATGCTGTATATCAGAGCTCTGAAAAACCCATCTCACTATGGTTTTTCATCTGGATTGAACAAAGATGGGATTGAAGCAAAATTACAAGAATTATGTTTGAAGAATCTGAAAGATTTATCATCACTAGACCTGATAAAGATGGATGAAGATGTTAATTTTAAACCAACAGAGGCAGGAAGACTAATGGCTTGGTATTATATTACATTTGAGACAGTCAAGAAATTTTGTGCAATCAGTGGAAAAGAAACTTTATTGGATTTAATTTCAATGATATCGAGCTGCAATGAGTTTCTAGATGTGCAGCTGAGGATAAGTGAAAAGAGAATACTGAACACCTTAAACAAAGACCCAAACCGGATAACTATCAGATTTCCAATGGCAGAAAGAATTAAAACAAGAGAAATGAAAGTAAACTGTCTTATTCAGGCTCAGCTAGGATGCATTCCTATACAAGATTTTGCTTTGACACAAGATACAGTGAAGATTTTCAGAAATGGCTCACGAATTGCAAGATGGTTGTCAGATTTTGTGGCTGCTCAGGAAAAGAAGTTTGCTGTGCTTTTAAACAGTGTGATTTTAACTAAATGTTTTAAGTGTAAACTCTGGGAAAACTCTAAACATGTATCAAAACAGCTGGATAAAATTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGTGCTTTTAAACAGTGTGA
59.56
ATAACAACCAGGTGAGCCGG
60.04
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTGTGCTTTTAAACAGTGTG
58.23
ATAACAACCAGGTGAGCCGG
60.04
150
PCR template sequence:
AAGTTTGCTGTGCTTTTAAACAGTGTGATTTTAACTAAATGTTTTAAGTGTAAACTCTGGGAAAACTCTAAACATGTATCAAAACAGCTGGATAAAATTGTCACTACCAGTACTCTAGCTATGGGCATGAACATGCCGGCTCACCTGGTTGTTATAAAGTCTACCATGCACTACAGTGGAGGTGTGTTTGAAGAGTACAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-150-5p(1), mmu-miR-143-3p(1), mmu-miR-127-3p(1), mmu-miR-669d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGGATAAAATTGTCACTACCAGTAC
siRNA sets
TAGTGACAATTTTATCCAG, GTAGTGACAATTTTATCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHFM1_981_ORF_1
0.8416
0.036604515
0.999970546
1941
ORF sequence:
ATGGGCATGAACATGCCGGCTCACCTGGTTGTTATAAAGTCTACCATGCACTACAGTGGAGGTGTGTTTGAAGAGTACAGCGAGACCGACATCCTGCAGATGATTGGGAGAGCTGGCAGACCCCAGTTTGACACTACAGCTACTGCAGTCATTATGACTCGACTAAGTACAAGAGAGAAGTACGTGCAGATGCTAGCTTGTAACGACACTGTAGAGAGCAGTTTGCACAGACATCTTATTGAACATTTAAATGCAGAAATAGTGCTGCATACCATCACAGACGTGAACATTGCTCTGGACTGGATCCGATCAACAATGCTGTATATCAGAGCTCTGAAAAACCCATCTCACTATGGTTTTTCATCTGGATTGAACAAAGATGGGATTGAAGCAAAATTACAAGAATTATGTTTGAAGAATCTGAAAGATTTATCATCACTAGACCTGATAAAGATGGATGAAGATGTTAATTTTAAACCAACAGAGGCAGGAAGACTAATGGCTTGGTATTATATTACATTTGAGACAGTCAAGAAATTTTGTGCAATCAGTGGAAAAGAAACTTTATTGGATTTAATTTCAATGATATCGAGCTGCAATGAGTTTCTAGATGTGCAGCTGAGGATAAGTGAAAAGAGAATACTGAACACCTTAAACAAAGACCCAAACCGGATAACTATCAGATTTCCAATGGCAGAAAGAATTAAAACAAGAGAAATGAAAGTAAACTGTCTTATTCAGGCTCAGCTAGGATGCATTCCTATACAAGATTTTGCTTTGACACAAGATACAGTGAAGATTTTCAGAAATGGCTCACGAATTGCAAGATGGTTGTCAGATTTTGTGGCTGCTCAGGAAAAGAAGTTTGCTGTGCTTTTAAACAGTGTGATTTTAACTAAATGTTTTAAGTGTAAACTCTGGGAAAACTCTAAACATGTATCAAAACAGCTGGATAAAATTGTCACTACCAGTACTCTAGCTATGGGCATGAACATGCCGGCTCACCTGGTTGTTATAAAGTCTACCATGCACTACAGTGGAGGTGTGTTTGAAGAGTACAGCGAGACCGACATCCTGCAGATGATTGGGAGAGCTGGCAGACCCCAGTTTGACACTACAGCTACTGCAGTCATTATGACTCGACTAAGTACAAGAGAGAAGTACGTGCAGATGCTAGCTTGTAACGACACTGTAGAGAGCAGTTTGCACAGACATCTTATTGAACATTTAAATGCAGAAATAGTGCTGCATACCATCACAGACGTGAACATTGCTCTGGACTGGATCCGATCAACAATGCTGTATATCAGAGCTCTGAAAAACCCATCTCACTATGGTTTTTCATCTGGATTGAACAAAGATGGGATTGAAGCAAAATTACAAGAATTATGTTTGAAGAATCTGAAAGATTTATCATCACTAGACCTGATAAAGATGGATGAAGATGTTAATTTTAAACCAACAGAGGCAGGAAGACTAATGGCTTGGTATTATATTACATTTGAGACAGTCAAGAAATTTTGTGCAATCAGTGGAAAAGAAACTTTATTGGATTTAATTTCAATGATATCGAGCTGCAATGAGTTTCTAGATGTGCAGCTGAGGATAAGTGAAAAGAGAATACTGAACACCTTAAACAAAGACCCAAACCGGATAACTATCAGATTTCCAATGGCAGAAAGAATTAAAACAAGAGAAATGAAAGTAAACTGTCTTATTCAGGCTCAGCTAGGATGCATTCCTATACAAGATTTTGCTTTGACACAAGATACAGTGAAGATTTTCAGAAATGGCTCACGAATTGCAAGATGGTTGTCAGATTTTGTGGCTGCTCAGGAAAAGAAGTTTGCTGTGCTTTTAAACAGTGTGATTTTAACTAAATGTTTTAAGTGTAAACTCTGGGAAAACTCTAAACATGTATCAAAACAGCTGGATAAAATT
Peptide sequence:
MGMNMPAHLVVIKSTMHYSGGVFEEYSETDILQMIGRAGRPQFDTTATAVIMTRLSTREKYVQMLACNDTVESSLHRHLIEHLNAEIVLHTITDVNIALDWIRSTMLYIRALKNPSHYGFSSGLNKDGIEAKLQELCLKNLKDLSSLDLIKMDEDVNFKPTEAGRLMAWYYITFETVKKFCAISGKETLLDLISMISSCNEFLDVQLRISEKRILNTLNKDPNRITIRFPMAERIKTREMKVNCLIQAQLGCIPIQDFALTQDTVKIFRNGSRIARWLSDFVAAQEKKFAVLLNSVILTKCFKCKLWENSKHVSKQLDKIVTTSTLAMGMNMPAHLVVIKSTMHYSGGVFEEYSETDILQMIGRAGRPQFDTTATAVIMTRLSTREKYVQMLACNDTVESSLHRHLIEHLNAEIVLHTITDVNIALDWIRSTMLYIRALKNPSHYGFSSGLNKDGIEAKLQELCLKNLKDLSSLDLIKMDEDVNFKPTEAGRLMAWYYITFETVKKFCAISGKETLLDLISMISSCNEFLDVQLRISEKRILNTLNKDPNRITIRFPMAERIKTREMKVNCLIQAQLGCIPIQDFALTQDTVKIFRNGSRIARWLSDFVAAQEKKFAVLLNSVILTKCFKCKLWENSKHVSKQLDKI
IRESfinder result
IRESfinder score
0.676690781
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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