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mmu_ciRnf213_2031
Basic information of circular RNA
PanCircBase ID:
mmu_ciRnf213_2031
mm39_Chr. Position ID:
chr11|119328954|119330985|+
Gene name:
Rnf213
Transcript:
ENSMUST00000093902.12
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
27
Exon/intron offsets:
0
Genomic length:
2031
Exon/intron sizes in nt:
2031
Flanking exon/introns:
chr11:119328954-119331014
Splice length:
2031
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGTATCAAGAAAAACACAGAGGTTTGGTGGGGGTTAAGCACTCCTATCCCACACTATTTATTTATTTATTTATTTATTTATGCCAACCCAATGCAAGCTTGAGATATCTGAGAAGGGGGTACCACAATCAAGGAAATCCCTCTATGAGATTGCCTGTAGGCAAGTTTGTAGGGCATTTCCTGGGCCCAGTCCTCATCAGGGGACAGTGTCACTGGTAGGACTGTGGTTCTGGAAGAAAGCAGGCTGAGCAAACCATGGTGAGCTGACCAGTAAGGTGGTGGTCCTTCCTGGCTTCTGCTTTAGTTCCTGCCTCCAGCTTCCTGTCTTGAGTTCATGTCCTAATTTTTCTCAGACAGACAGTGTAACATGTGAGTTGTAAGGTGAACTAAACCCTTTCCTCTCCAAGTAGCTTTTGGTCATGGTGTTTTATCACAGCAATAGAAAATGATACCAGGTTCATGGGATAGTGCTGAGATAGACCTAACCATGTATTTTGGGGAGAATTATGGTGACATTTGAGCTCTGAGCCATCAGACCTCAGTGCAGTATTTTATGGGAGAACAACACAGACCAGAGAGGCCTGGCTTGTGAAGTTTAGAGGGAAGTAAAGACTCATATCAGGGCCATTTGAGTGATGTTTTGAATTAAGCAACTGTGGTTCTCGTTAGCTGGGAGTGAAGCATTAACGAGAGACCGGAACACTAAGTTGAAACCTTTGCTTGTCTTGGATAATCCATGTTGGTCAGCTGGGGCTGAGAAATTACCTCTGACTGAGAAGAGACTAGCGGCACTGAGGGGAAATCTTCTGGGAAGTGTTTGCTCAGGATCAGCACACAGATGCTGTGGCGCAGAGGTTGCTGAGCCTGTTTCTCAGGCTTGCAGCTGAGAGCTCTGTTAAGAGCTGCTGGTCTCACCGATTCAGGATAAACTTGAAGTAAACTTAATACTATAAAAGATTTCTTCATAAACTTGCTTATGAAATATTAAGTTATACAATTAAAATTTAGCTATAGGAGTCCCGCCTCCGATATGACTGGAAGATTAGTGTCCTAACCAGGTTTGTTAGAAATAGAACCGGGAGGAAAGAAAATTCTGTGCCGGCTTAAAGCTAAGGGGTTACTGAGAGCTTATTTATTGAGACTGACCTCTAGTTAGGCTCCAGTCCCATAACAAAAGGAGACAACCTTAACTTACAACTGGTTCTTAGGTCCATCCCCTTACGAAAACACATGAGGCTCATGGGGGTAGCACAGGGTTCTGGTCTGCCATTAAGTTTCCTATGCTCTTTACTGTGAAAAGTACAAATCTGCCAGGTTGGCAAGATGACCCTGGATAACAAGTATTCACAAAGAGCAACACTGATGTGTATCTGTACACCTGATCATCTCTGTTCAAATTGTTCAAAGTGCAACCTGGGGCCGGAACCTGAAAGACATCAAAGATAACAGCATAGCTGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGATAGCCAGGGCTACACAGAGAAACTCTGTCTCCAAAACAAAATAAAAAAGATAACAGCATATGTGGAATGTATAAGCCTAAGGTGCGTAGATGTTAGTAAATGCAGAGCCTGGCACACACCTATATTAAGGAGACTTTTCTTGTTGGTATCCAAGTGTTCAGGGAAGGCGTATTAGTTCTATAACCTCTATAACCTCAGGCACCAGAGGCAATGAGGTCCTCTTGGACCTGAAGAGGAACTTGGTACTTGAAGAGGTTTGGAGCTCACACATACTCACAGGTGTATGTGCATAGTGAAGACACAAGCCCTTGATTGTGTTAGAAAATGCATCTTTGTTAGGGATGTGTCTTCTAATTTAGTTCTCTAAACCCTTAGCAGGCAAAAGTTTCCAGTCCATGGGGACAAATTAAGTTCAGTGCAGACTGTGTGGAGAGTTAAGACAGAAAGACAGCGGTTAGGGAATTCAGTGATCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGCAAAAGTTTCCAGTCC
60.27
GAGTGCTTAACCCCCACCAA
59.89
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGCAAAAGTTTCCAGTCC
60.27
GCTTAACCCCCACCAAACCT
60.18
141
PCR template sequence:
AGCAGGCAAAAGTTTCCAGTCCATGGGGACAAATTAAGTTCAGTGCAGACTGTGTGGAGAGTTAAGACAGAAAGACAGCGGTTAGGGAATTCAGTGATCAGTGTGTATCAAGAAAAACACAGAGGTTTGGTGGGGGTTAAGCACTCCTATCCCACACTATTTATTTATTTATTTATTTATTTATGCCAACCCAATGCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-3087-3p(2), mmu-miR-490-3p(2), mmu-miR-137-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-26a-5p(1), mmu-miR-146a-5p(1), mmu-miR-33-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-495-3p(1), mmu-miR-541-5p(1), mmu-miR-669d-5p(1), mmu-miR-484(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTCAGTGATCAGTGTGTATCAAGA
siRNA sets
ATACACACTGATCACTGAA, GATACACACTGATCACTGA
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
0.7477625
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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