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mmu_circRc3h2_415
Basic information of circular RNA
PanCircBase ID:
mmu_circRc3h2_415
mm39_Chr. Position ID:
chr2|37301151|37304824|-
Gene name:
Rc3h2
Transcript:
ENSMUST00000112934.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
4,3
Exon/intron offsets:
0,3376
Genomic length:
3673
Exon/intron sizes in nt:
1,18,297
Flanking exon/introns:
chr2:37299679-37301151|chr2:37304824-37309443
Splice length:
415
Other database IDs:
CIRCpedia: MMU_CIRCpedia_18551, circAtlas: mmu-Rc3h2_0005
circBase: hsa_circ_0088397, circAtlas: hsa-RC3H2_0040, CIRCpedia: HSA_CIRCpedia_62621
Human Ortholog IDs:
Mature spliced Sequence:
CTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAACCCGAGCATCAGCTTCCACAATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTCTGTCCTGTCCAATCTGCTATAATGAATTTGATGAGAATGTGCACAAACCCATCAGTTTAGGTTGTTCACACACAGTTTGCAAGACCTGCTTGAATAAACTTCACCGAAAAGCGTGTCCTTTTGACCAGACTGCCATAAACACAGACATTGATGTGCTCCCTGTCAACTTTGCACTTCTTCAGTTAGTTGGAGCCCAGGTACCAGATCATCAGTCAATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCGTAGAGGACTTGGCAC
60.11
ACTCTGTCCATTGAGCTGCC
60.04
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCGTAGAGGACTTGGCAC
60.11
TCTGTCCATTGAGCTGCCTG
60.04
145
PCR template sequence:
ATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAGCTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAACCCGAGCATCAGCTTCCACAATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-140-5p(1), mmu-miR-130a-3p(1), mmu-miR-431-5p(1), mmu-miR-130b-3p(1), mmu-miR-721(1), mmu-miR-125b-1-3p(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTGGAGGTAAAGCTTAAAAAACACT
siRNA sets
TTTTTTAAGCTTTACCTCC,TTTTTAAGCTTTACCTCCA,TTTTAAGCTTTACCTCCAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRC3H2_415_ORF_1
0.8596
-0.023969139
0.230163254
354
ORF sequence:
ATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTCTGTCCTGTCCAATCTGCTATAATGAATTTGATGAGAATGTGCACAAACCCATCAGTTTAGGTTGTTCACACACAGTTTGCAAGACCTGCTTGAATAAACTTCACCGAAAAGCGTGTCCTTTTGACCAGACTGCCATAAACACAGACATTGATGTGCTCCCTGTCAACTTTGCACTTCTTCAGTTAGTTGGAGCCCAGGTACCAGATCATCAGTCAATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAGCTTAA
Peptide sequence:
MPVQAAQWTEFLSCPICYNEFDENVHKPISLGCSHTVCKTCLNKLHRKACPFDQTAINTDIDVLPVNFALLQLVGAQVPDHQSIKLSNLGENKHYEVAKKCVEDLALYLKPLSGGKA
IRESfinder result
IRESfinder score
0.745114797
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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