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mmu_circRap1a_611
Basic information of circular RNA
PanCircBase ID:
mmu_circRap1a_611
mm39_Chr. Position ID:
chr3|105639271|105657644|-
Gene name:
Rap1a
Transcript:
ENSMUST00000090678.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,6,5,4,3,2
Exon/intron offsets:
0,5799,7558,9390,13948,18289
Genomic length:
18373
Exon/intron sizes in nt:
116,144,141,57,69,84
Flanking exon/introns:
chr3:105636280-105639271|chr3:105657644-105708554
Splice length:
611
Other database IDs:
circBase: hsa_circ_0110426, circAtlas: hsa-RAP1A_0001, CIRCpedia: HSA_CIRCpedia_27288
Human Ortholog IDs:
Mature spliced Sequence:
ATTGTCAATATTTAAACAGAGCGCATCATGCGTGAGTACAAGCTAGTAGTCCTTGGTTCAGGAGGCGTGGGGAAGTCTGCTCTGACAGTTCAGTTTGTTCAGGGGATTTTTGTTGAAAAATATGACCCAACGATAGAAGATTCCTACAGAAAGCAAGTCGAGGTAGATTGCCAACAGTGCATGCTGGAGATCCTGGACACTGCAGGAACCGAGCAATTTACAGCAATGAGGGATTTGTATATGAAGAATGGCCAAGGGTTTGCACTAGTTTATTCAATTACAGCTCAGTCTACGTTTAATGATTTACAAGACTTGAGAGAACAGATTTTACGGGTTAAAGACACAGAAGATGTTCCAATGATTTTGGTTGGCAATAAATGTGACTTGGAAGATGAACGGGTAGTTGGCAAAGAACAAGGCCAGAATTTAGCAAGACAGTGGTGTAACTGTGCCTTTTTAGAATCTTCTGCAAAGTCAAAGATCAACGTTAATGAGATATTTTATGACCTGGTCAGACAGATAAATAGAAAAACACCAGTGGAAAAGAAGAAGCCTAAAAAGAAATCATGTTTGCTGCTCTAGACCTGAAGTCAGCAGCAGCTCTGAGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCAGTGGAAAAGAAGAAGCCT
59.82
GTCAGAGCAGACTTCCCCAC
60.04
164
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACCAGTGGAAAAGAAGAAGCC
59.71
GTCAGAGCAGACTTCCCCAC
60.04
165
PCR template sequence:
TCAGACAGATAAATAGAAAAACACCAGTGGAAAAGAAGAAGCCTAAAAAGAAATCATGTTTGCTGCTCTAGACCTGAAGTCAGCAGCAGCTCTGAGCCAGATTGTCAATATTTAAACAGAGCGCATCATGCGTGAGTACAAGCTAGTAGTCCTTGGTTCAGGAGGCGTGGGGAAGTCTGCTCTGACAGTTCAGTTTGTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-19b-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-19a-3p(1), mmu-miR-301a-3p(1), mmu-miR-3065-5p(1), mmu-miR-99a-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTCTGAGCCAGATTGTCAATATTT
siRNA sets
AAATATTGACAATCTGGCT, ATATTGACAATCTGGCTCA, AATATTGACAATCTGGCTC
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
0.634174553
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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