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mmu_circRc3h2_1159
Basic information of circular RNA
PanCircBase ID:
mmu_circRc3h2_1159
mm39_Chr. Position ID:
chr2|37289832|37304824|-
Gene name:
Rc3h2
Transcript:
ENSMUST00000112934.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
8,7,6,5,4,3
Exon/intron offsets:
0,708,5423,9613,11319,14695
Genomic length:
14992
Exon/intron sizes in nt:
1,33,20,11,76,23,41,18,000
Flanking exon/introns:
chr2:37289717-37289832|chr2:37304824-37309443
Splice length:
1159
Other database IDs:
CIRCpedia: MMU_CIRCpedia_18545, circAtlas: mmu-Rc3h2_0029
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_62615
Human Ortholog IDs:
Mature spliced Sequence:
CTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAACCCGAGCATCAGCTTCCACAATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTCTGTCCTGTCCAATCTGCTATAATGAATTTGATGAGAATGTGCACAAACCCATCAGTTTAGGTTGTTCACACACAGTTTGCAAGACCTGCTTGAATAAACTTCACCGAAAAGCGTGTCCTTTTGACCAGACTGCCATAAACACAGACATTGATGTGCTCCCTGTCAACTTTGCACTTCTTCAGTTAGTTGGAGCCCAGGTACCAGATCATCAGTCAATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAGGTGTAGCTAGTTTGAACCAGAGTGCCCTGAGCCGTCCAATGCAAAGGAAACTAGTTACACTTGTAAACTGTCAACTGGTGGAAGAAGAAGGTCGTGTCAGAGCTATGCGAGCGGCCCGTTCACTAGGAGAAAGAACTGTGACAGAACTGATACTGCAGCACCAGAACCCTCAGCAGCTGTCTGCCAACCTGTGGGCTGCTGTCAGGGCTCGAGGATGCCAGTTTCTAGGGCCAGCTATGCAAGAAGAAGCCTTGAAGTTGGTATTGCTGGCATTAGAAGATGGTTCTGCTCTCTCTAGGAAAGTTCTAGTACTTTTTGTTGTGCAAAGACTAGAACCAAGATTTCCTCAGGCATCAAAAACAAGTATTGGCCATGTTGTGCAGCTATTGTACCGAGCTTCTTGTTTTAAGGTTACTAAAAGGGATGAAGACTCTTCCCTGATGCAGCTAAAGGAGGAATTTCGGAGTTACGAGGCACTACGCAGAGAACATGATGCCCAGATTGTTCATATTGCCATGGAAGCAGGACTCCGTATTTCACCTGAGCAGTGGTCTTCACTGCTGTATGGGGACTTGGCTCATAAATCACACATGCAGTCTATCATTGATAAGCTACAGTCTCCAGAATCATTTGCAAAGAGTGTCCAGGAATTGACAATTGTTTTGCAGCGAACTGGTGACCCTGCTAATTTAAATAGGCTGAGACCTCATTTAGAGCTTCTTGCAAACATAGACCCTAATCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAACTGGTGACCCTGCTAA
59.68
ACTCTGTCCATTGAGCTGCC
60.04
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAACTGGTGACCCTGCTAA
59.68
TCTGTCCATTGAGCTGCCTG
60.04
171
PCR template sequence:
CAGGAATTGACAATTGTTTTGCAGCGAACTGGTGACCCTGCTAATTTAAATAGGCTGAGACCTCATTTAGAGCTTCTTGCAAACATAGACCCTAATCCAGCTTAAAAAACACTACACATCAAAATAATGATCTGCTAGACTGCTAACCCGAGCATCAGCTTCCACAATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-140-5p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-130a-3p(1), mmu-miR-138-5p(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), mmu-miR-1187(1), mmu-miR-3065-5p(1), mmu-miR-3470b(1)
siRNAs for circular RNA silencing
Junction sequence
GACCCTAATCCAGCTTAAAAAACACT
siRNA sets
TTTTTTAAGCTGGATTAGG, TTTTTAAGCTGGATTAGGG, GTTTTTTAAGCTGGATTAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRC3H2_1159_ORF_1
1.1026
0.038396337
0.992105717
1098
ORF sequence:
ATGCCTGTGCAGGCAGCTCAATGGACAGAGTTTCTGTCCTGTCCAATCTGCTATAATGAATTTGATGAGAATGTGCACAAACCCATCAGTTTAGGTTGTTCACACACAGTTTGCAAGACCTGCTTGAATAAACTTCACCGAAAAGCGTGTCCTTTTGACCAGACTGCCATAAACACAGACATTGATGTGCTCCCTGTCAACTTTGCACTTCTTCAGTTAGTTGGAGCCCAGGTACCAGATCATCAGTCAATAAAGTTAAGTAATCTAGGTGAGAATAAACACTATGAAGTGGCAAAAAAATGCGTAGAGGACTTGGCACTCTACTTAAAACCACTAAGTGGAGGTAAAGGTGTAGCTAGTTTGAACCAGAGTGCCCTGAGCCGTCCAATGCAAAGGAAACTAGTTACACTTGTAAACTGTCAACTGGTGGAAGAAGAAGGTCGTGTCAGAGCTATGCGAGCGGCCCGTTCACTAGGAGAAAGAACTGTGACAGAACTGATACTGCAGCACCAGAACCCTCAGCAGCTGTCTGCCAACCTGTGGGCTGCTGTCAGGGCTCGAGGATGCCAGTTTCTAGGGCCAGCTATGCAAGAAGAAGCCTTGAAGTTGGTATTGCTGGCATTAGAAGATGGTTCTGCTCTCTCTAGGAAAGTTCTAGTACTTTTTGTTGTGCAAAGACTAGAACCAAGATTTCCTCAGGCATCAAAAACAAGTATTGGCCATGTTGTGCAGCTATTGTACCGAGCTTCTTGTTTTAAGGTTACTAAAAGGGATGAAGACTCTTCCCTGATGCAGCTAAAGGAGGAATTTCGGAGTTACGAGGCACTACGCAGAGAACATGATGCCCAGATTGTTCATATTGCCATGGAAGCAGGACTCCGTATTTCACCTGAGCAGTGGTCTTCACTGCTGTATGGGGACTTGGCTCATAAATCACACATGCAGTCTATCATTGATAAGCTACAGTCTCCAGAATCATTTGCAAAGAGTGTCCAGGAATTGACAATTGTTTTGCAGCGAACTGGTGACCCTGCTAATTTAAATAGGCTGAGACCTCATTTAGAGCTTCTTGCAAACATAGACCCTAATCCAGCTTAA
Peptide sequence:
MPVQAAQWTEFLSCPICYNEFDENVHKPISLGCSHTVCKTCLNKLHRKACPFDQTAINTDIDVLPVNFALLQLVGAQVPDHQSIKLSNLGENKHYEVAKKCVEDLALYLKPLSGGKGVASLNQSALSRPMQRKLVTLVNCQLVEEEGRVRAMRAARSLGERTVTELILQHQNPQQLSANLWAAVRARGCQFLGPAMQEEALKLVLLALEDGSALSRKVLVLFVVQRLEPRFPQASKTSIGHVVQLLYRASCFKVTKRDEDSSLMQLKEEFRSYEALRREHDAQIVHIAMEAGLRISPEQWSSLLYGDLAHKSHMQSIIDKLQSPESFAKSVQELTIVLQRTGDPANLNRLRPHLELLANIDPNPA
IRESfinder result
IRESfinder score
0.659427247
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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