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mmu_ciMbnl1_1162
Basic information of circular RNA
PanCircBase ID:
mmu_ciMbnl1_1162
mm39_Chr. Position ID:
chr3|60520941|60522103|+
Gene name:
Mbnl1
Transcript:
ENSMUST00000193647.6
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
1162
Exon/intron sizes in nt:
1162
Flanking exon/introns:
chr3:60520941-60522103
Splice length:
1162
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTGGAGACAGCAGTGCCCTCCTGTCAGCAATCAGAAAAGATAGTGAACAATTTCTCTACTGCCAGCTATTCATCTATTAACCTCTTCCTCCCGTTTTGCTGAAGATATGTTTGTTCAGGTATCCCACACAATACATAAAGAAGCTACCATTCACAGACGCAAGGATAACTCCTCAAATGTTGCTCATCCTCTTAGCCTAACCCCTAAGACTGTCTCATTCTGGATGTAGGGTTTCTGAAATTCCTGCTTCATAAGGAACCACTTGTCGCCTTTCTGATTGAACGACACTGCCATTTCCAGTCTCTGATTTCTGTATGCCATCCAGCTGGCCCTTGTTCTCCTTGAGTGTGTTCTTCCCCACATCAAGGCTCTTCTTTACATTTATCTTGCCTTTAATAACATCATCTGAAACTATTTAGGAGAATAGCTTCAACAAAATTGTTTTTAAATTAGCTGCAATGATCCTTTTGAATGATCCGCTGTCGAGATCGTGTGAAGGCCTACTGTGGCAGAAACATGATTATTACAGTGCCAAATATTGACTAAGCCACTATACAGGGAAGAGAAGAGCACTAGCACTCAAGGAGTGTTTAAAAAATGAATAAATAAGTAAGGATCATTTAGGGTAGATGCTAAGTGGTTTATCTTAAGATCAACTTCAATGAGACCTAGTAGATGAGTTTAAGGAGGCCATTTCTTCTTGGCTTAGCTGTTTTAACGCTGTCCTTTTTAATATAAATATATAACTTATTCTTTAAATATTCATACAAAAATCATTGTCATGGCACAGTAAAATGATCATGAGAGAGGTCTTTTCTGTGTTTGTTTATGGATACTTGAGCAAAAATACAGAAGGCAGACTCTCTCCTTTTCTCTTTCTTTCACCACCCCCCCTTTTTTTTCTTTAGAGTATTATTTGAAATTAACTACAAAGAGGAATTATCCTCCAATAACAACTCAATAGTGCCTTTATTGTGCATGCTTAGTCTTGTTATTCGTTGTATATGGCATTCCGATGATTTGTTTTTTTATTTGTTTTTTCTCACCTACCCAAAATGCACTGCTGCCCCCATGATGCACCTCTGCTTGCTGTTTATGTTAATGCGCTTGAACCCCACTGGCCCATTGCCATCATGTGCTCGCTGCCTGCTAATTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACTGCTGCCCCCATGATG
61.13
TTCTGATTGCTGACAGGAGGG
59.72
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACTGCTGCCCCCATGAT
59.72
TTCTGATTGCTGACAGGAGGG
59.72
140
PCR template sequence:
CACTGCTGCCCCCATGATGCACCTCTGCTTGCTGTTTATGTTAATGCGCTTGAACCCCACTGGCCCATTGCCATCATGTGCTCGCTGCCTGCTAATTAAGGTGAGTGGAGACAGCAGTGCCCTCCTGTCAGCAATCAGAAAAGATAGTGAACAATTTCTCTACTGCCAGCTATTCATCTATTAACCTCTTCCTCCCGTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-34c-5p(1), mmu-miR-30e-5p(1), mmu-miR-34a-5p(1), mmu-miR-31-5p(1), mmu-miR-26a-5p(1), mmu-miR-495-3p(1), mmu-miR-26b-5p(1), mmu-miR-96-5p(1), mmu-miR-483-5p(1), mmu-miR-382-5p(1), mmu-miR-34b-5p(1), mmu-miR-383-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-539-5p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTGCTAATTAAGGTGAGTGGAGACA
siRNA sets
TCCACTCACCTTAATTAGC, ACTCACCTTAATTAGCAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIMBNL1_1162_ORF_1
0.568
-0.152867025
0.049216158
264
ORF sequence:
ATGCTTAGTCTTGTTATTCGTTGTATATGGCATTCCGATGATTTGTTTTTTTATTTGTTTTTTCTCACCTACCCAAAATGCACTGCTGCCCCCATGATGCACCTCTGCTTGCTGTTTATGTTAATGCGCTTGAACCCCACTGGCCCATTGCCATCATGTGCTCGCTGCCTGCTAATTAAGGTGAGTGGAGACAGCAGTGCCCTCCTGTCAGCAATCAGAAAAGATAGTGAACAATTTCTCTACTGCCAGCTATTCATCTATTAA
Peptide sequence:
MLSLVIRCIWHSDDLFFYLFFLTYPKCTAAPMMHLCLLFMLMRLNPTGPLPSCARCLLIKVSGDSSALLSAIRKDSEQFLYCQLFIY
IRESfinder result
IRESfinder score
0.914673264
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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