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mmu_circLifr_404
Basic information of circular RNA
PanCircBase ID:
mmu_circLifr_404
mm39_Chr. Position ID:
chr15|7183867|7189002|+
Gene name:
Lifr
Transcript:
ENSMUST00000228723.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,2769,5004
Genomic length:
5135
Exon/intron sizes in nt:
161,112,131
Flanking exon/introns:
chr15:7120229-7183867|chr15:7189002-7194009
Splice length:
404
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39161, circAtlas: mmu-Lifr_0001
circBase: hsa_circ_0129047, circAtlas: hsa-LIFR_0007, CIRCpedia: HSA_CIRCpedia_116798
Human Ortholog IDs:
Mature spliced Sequence:
GGCTGACTGAACAGCAAGGACAATGGCAGCTTACTCATGGTGGAGACAGCCATCGTGGATGGTAGACAATAAAAGATCGAGGATGACTCCAAACCTGCCATGGCTCCTGTCAGCTCTGACCCTCCTGCATCTGACGATGCATGCAAACGGTCTGAAGAGAGGGGTACAAGACTTGAAATGCACAACCAACAACATGCGAGTGTGGGACTGCACGTGGCCAGCTCCCCTCGGGGTCAGCCCTGGAACTGTTAAAGATATTTGCATTAAAGACAGGTTCCATTCTTGTCACCCATTAGAGACAACAAACGTTAAAATTCCAGCTCTTTCACCTGGTGATCACGAAGTCACAATAAATTATCTAAATGGCTTTCAGAGTAAATTCACGTTGAATGAAAAAGATGTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCTCTTTCACCTGGTGA
59.6
CATCCACGATGGCTGTCTCC
60.53
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAGCTCTTTCACCTGGTG
59.6
CATCCACGATGGCTGTCTCC
60.53
150
PCR template sequence:
AACGTTAAAATTCCAGCTCTTTCACCTGGTGATCACGAAGTCACAATAAATTATCTAAATGGCTTTCAGAGTAAATTCACGTTGAATGAAAAAGATGTCTGGCTGACTGAACAGCAAGGACAATGGCAGCTTACTCATGGTGGAGACAGCCATCGTGGATGGTAGACAATAAAAGATCGAGGATGACTCCAAACCTGCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-22-3p(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAAAAGATGTCTGGCTGACTGAACA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCLIFR_404_ORF_1
0.6023
-0.040357526
0.253265699
447
ORF sequence:
ATGGCAGCTTACTCATGGTGGAGACAGCCATCGTGGATGGTAGACAATAAAAGATCGAGGATGACTCCAAACCTGCCATGGCTCCTGTCAGCTCTGACCCTCCTGCATCTGACGATGCATGCAAACGGTCTGAAGAGAGGGGTACAAGACTTGAAATGCACAACCAACAACATGCGAGTGTGGGACTGCACGTGGCCAGCTCCCCTCGGGGTCAGCCCTGGAACTGTTAAAGATATTTGCATTAAAGACAGGTTCCATTCTTGTCACCCATTAGAGACAACAAACGTTAAAATTCCAGCTCTTTCACCTGGTGATCACGAAGTCACAATAAATTATCTAAATGGCTTTCAGAGTAAATTCACGTTGAATGAAAAAGATGTCTGGCTGACTGAACAGCAAGGACAATGGCAGCTTACTCATGGTGGAGACAGCCATCGTGGATGGTAG
Peptide sequence:
MAAYSWWRQPSWMVDNKRSRMTPNLPWLLSALTLLHLTMHANGLKRGVQDLKCTTNNMRVWDCTWPAPLGVSPGTVKDICIKDRFHSCHPLETTNVKIPALSPGDHEVTINYLNGFQSKFTLNEKDVWLTEQQGQWQLTHGGDSHRGW
IRESfinder result
IRESfinder score
0.45961715
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
RPF, cORF, MS, m6A
mmu_circLifr_001
Evidence
Peptide sequence:
MAAYSWWRQPSWMVDNKRSRMTPNLPWLLSALTLLHLTMHANGLKRGVQDLKCTTNNMRVWDCTWPAPLGVSPGTVKDICIKDRFHSCHPLETTNVKIPALSPGDHEVTINYLNGFQSKFTLNEKDVWLTEQQGQWQLTHGGDSHRGW*
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