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mmu_circTnpo1_323
Basic information of circular RNA
PanCircBase ID:
mmu_circTnpo1_323
mm39_Chr. Position ID:
chr13|99006747|99015234|-
Gene name:
Tnpo1
Transcript:
ENSMUST00000109399.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,5364,8380
Genomic length:
8487
Exon/intron sizes in nt:
82,134,107
Flanking exon/introns:
chr13:99003676-99006747|chr13:99015234-99021022
Splice length:
323
Other database IDs:
CIRCpedia: MMU_CIRCpedia_212189, circAtlas: mmu-Tnpo1_0002
circBase: hsa_circ_0072917, circAtlas: hsa-TNPO1_0079, CIRCpedia: HSA_CIRCpedia_52480
Human Ortholog IDs:
Mature spliced Sequence:
GTATTTTAATTACAACCATAGCCTCCAAGGGAGAGCTGCAGAATTGGCCTGATCTCTTACCAAAACTCTGTAGCCTGCTGGATTCCGAAGACTACAACACTTGTGAGGGAGCCTTCGGTGCCCTTCAGAAGATATGTGAGGACTCTGCAGAGATTTTAGACAGTGATGTCTTAGATCGCCCTCTCAACATCATGATCCCCAAGTTTTTACAGTTTTTCAAGCACAGCAGTCCCAAAATAAGGTCTCATGCTGTTGCATGTGTCAATCAGTTCATCATCAGTCGGACCCAGGCGCTCATGCTGCACATCGATTCCTTCATTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATCATCAGTCGGACCCAGG
59.89
TTCGGAATCCAGCAGGCTAC
59.82
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATCATCAGTCGGACCCAGG
59.89
CTTCGGAATCCAGCAGGCTA
59.53
142
PCR template sequence:
CAGCAGTCCCAAAATAAGGTCTCATGCTGTTGCATGTGTCAATCAGTTCATCATCAGTCGGACCCAGGCGCTCATGCTGCACATCGATTCCTTCATTGAGGTATTTTAATTACAACCATAGCCTCCAAGGGAGAGCTGCAGAATTGGCCTGATCTCTTACCAAAACTCTGTAGCCTGCTGGATTCCGAAGACTACAACAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-214-3p(1), mmu-miR-218-5p(1), mmu-miR-339-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCCTTCATTGAGGTATTTTAATTAC
siRNA sets
AATTAAAATACCTCAATGA, TAAAATACCTCAATGAAGG, AAAATACCTCAATGAAGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTNPO1_323_ORF_1
1.0583
0.103489578
0.135928825
141
ORF sequence:
ATGATCCCCAAGTTTTTACAGTTTTTCAAGCACAGCAGTCCCAAAATAAGGTCTCATGCTGTTGCATGTGTCAATCAGTTCATCATCAGTCGGACCCAGGCGCTCATGCTGCACATCGATTCCTTCATTGAGGTATTTTAA
Peptide sequence:
MIPKFLQFFKHSSPKIRSHAVACVNQFIISRTQALMLHIDSFIEVF
IRESfinder result
IRESfinder score
0.728208525
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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