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mmu_ciHook1_843
Basic information of circular RNA
PanCircBase ID:
mmu_ciHook1_843
mm39_Chr. Position ID:
chr4|95880436|95881279|+
Gene name:
Hook1
Transcript:
ENSMUST00000030306.14
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
843
Exon/intron sizes in nt:
843
Flanking exon/introns:
chr4:95880436-95881302
Splice length:
843
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACCGGAAACACCTGATCTTAAACAAAAGTGCCAAGAGTTTGACTACTTGTTTTTTTAAGCATCATGTTGGAATGTAATTTATAATTATAATAATTATGTTGCCACTTATAGAGCACATAACACTTGTGAAAATGAAAAGGTCTAAGGATTAAATGCATTGGCTTACCAAAGGAAGAAAGAAGATAGTTTTCATTTTGAAACTTTGAATTGATTACCTTTATAAATAGAATGTATTGCATAATAATTGGTGGCCTCTGAACTGATTTTGTTAGTAAAGGATTTTTTTATATATATATTTCAACATTACAGAAATTATTTGAAAGTTTCTTGGAAGTTTTAATACTATGAGAATTTTCAGTGCTTTATTCACCCAGTATCCTTAGAAACTTATTGTTTCAAGAAAATAGAAAAAAGGCCAGAGAAAGTCAAAGTCATTACATTTGTTATTCATTTGTGAAAGTGCAGTTCATATTGTGAATCTAAGTGATAACATACTATCACAAACTTTGTTCAGATAGTCTGGCTTCCATTCAGATTGGGTAAGTAATTTTGCCTATATCAATCAGTCTTCTGGGCTAACATAATCCTGTTTACAGTTTCCTAGGCAAGCATGGGTCCCCTTTAACAAATCCTTGTTTTTCTAATATGAGGTCAATTAAACATCAAGCACAACCAACCAGAATTTTGAGAAGGGACCAGAATATTGCTGACTTGGTGTTAGTCAGTGTTAGTGACTCATGATTTCTTAATTTACTTGAGTTATTTCATGAAGGTATTTCGAATTAACTTTTCTTTAAATAACAGTATAAGTTCTTTGTAGCCTACATAGATGAGTAATCTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGAGTTATTTCATGAAGGTATTTCG
57.29
ACAAGTAGTCAAACTCTTGGCAC
59.12
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGAGTTATTTCATGAAGGTATTTCGA
57.56
AACAAGTAGTCAAACTCTTGGCAC
59.66
140
PCR template sequence:
TTTCTTAATTTACTTGAGTTATTTCATGAAGGTATTTCGAATTAACTTTTCTTTAAATAACAGTATAAGTTCTTTGTAGCCTACATAGATGAGTAATCTAGTACCGGAAACACCTGATCTTAAACAAAAGTGCCAAGAGTTTGACTACTTGTTTTTTTAAGCATCATGTTGGAATGTAATTTATAATTATAATAATTATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-26a-5p(1), mmu-miR-26b-5p(1), mmu-miR-218-5p(1), mmu-miR-340-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GATGAGTAATCTAGTACCGGAAACAC
siRNA sets
TTCCGGTACTAGATTACTC, GTTTCCGGTACTAGATTAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.937807938
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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