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mmu_circNhlrc2_352
Basic information of circular RNA
PanCircBase ID:
mmu_circNhlrc2_352
mm39_Chr. Position ID:
chr19|56563189|56576701|+
Gene name:
Nhlrc2
Transcript:
ENSMUST00000071423.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,5,6
Exon/intron offsets:
0,1397,13412
Genomic length:
13512
Exon/intron sizes in nt:
12,21,30,100
Flanking exon/introns:
chr19:56559303-56563189|chr19:56576701-56580007
Splice length:
352
Other database IDs:
circAtlas: mmu-Nhlrc2_0004
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_129313
Human Ortholog IDs:
Mature spliced Sequence:
GACCTAACCCTGGAAGGAAAGATGGGATGTTTTCAGAGTCGTCTTTTAATTCTCCACAGGGTGTAGCTATAGCAGATAATGTCATCTATGTGGCCGACACTGAGAACCACCTTATAAGAAAGATAGACCTGGAAGCTGAGAAGGTGACCACTGTGGCTGGTGTCGGTATTCAAGGGACAGATACAGAAGGGGGCGAGGAGGGAGACAAGCAGCCCATCAGCTCCCCGTGGGACGTTGCGCTTGGGACCTCAGGTTCAGAGGTCCAAAGAAATGACATCCTGTGGATAGCCATGGCAGGGACTCATCAGATATGGGCACTCCTCCTAGACTCTGGCACACTGCCAAAGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGCACTCCTCCTAGACTC
60.03
GTGTCGGCCACATAGATGACA
60.13
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GATAGCCATGGCAGGGACTC
59.96
GTGTCGGCCACATAGATGACA
60.13
169
PCR template sequence:
GTTCAGAGGTCCAAAGAAATGACATCCTGTGGATAGCCATGGCAGGGACTCATCAGATATGGGCACTCCTCCTAGACTCTGGCACACTGCCAAAGAAAAGGACCTAACCCTGGAAGGAAAGATGGGATGTTTTCAGAGTCGTCTTTTAATTCTCCACAGGGTGTAGCTATAGCAGATAATGTCATCTATGTGGCCGACAC
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-27b-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCAAAGAAAAGGACCTAACCCTGG
siRNA sets
GTTAGGTCCTTTTCTTTGG, TTAGGTCCTTTTCTTTGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNHLRC2_352_ORF_1
1.0928
0.179610713
0.477525006
333
ORF sequence:
ATGTTTTCAGAGTCGTCTTTTAATTCTCCACAGGGTGTAGCTATAGCAGATAATGTCATCTATGTGGCCGACACTGAGAACCACCTTATAAGAAAGATAGACCTGGAAGCTGAGAAGGTGACCACTGTGGCTGGTGTCGGTATTCAAGGGACAGATACAGAAGGGGGCGAGGAGGGAGACAAGCAGCCCATCAGCTCCCCGTGGGACGTTGCGCTTGGGACCTCAGGTTCAGAGGTCCAAAGAAATGACATCCTGTGGATAGCCATGGCAGGGACTCATCAGATATGGGCACTCCTCCTAGACTCTGGCACACTGCCAAAGAAAAGGACCTAA
Peptide sequence:
MFSESSFNSPQGVAIADNVIYVADTENHLIRKIDLEAEKVTTVAGVGIQGTDTEGGEEGDKQPISSPWDVALGTSGSEVQRNDILWIAMAGTHQIWALLLDSGTLPKKRT
IRESfinder result
IRESfinder score
0.438048238
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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