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mmu_circUbr3_822
Basic information of circular RNA
PanCircBase ID:
mmu_circUbr3_822
mm39_Chr. Position ID:
chr2|69808062|69824156|+
Gene name:
Ubr3
Transcript:
ENSMUST00000055758.16
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
24,25,26,27,28,29
Exon/intron offsets:
0,1600,5409,11067,13706,15957
Genomic length:
16094
Exon/intron sizes in nt:
89,150,134,111,201,137
Flanking exon/introns:
chr2:69803953-69808062|chr2:69824156-69830801
Splice length:
822
Other database IDs:
circBase: mmu_circ_0010140, CIRCpedia: MMU_CIRCpedia_27340, circAtlas: mmu-Ubr3_0067
circBase: hsa_circ_0056994
Human Ortholog IDs:
Mature spliced Sequence:
GCGACAAAAGGCTAGAGAAAGGCAGCAGAAATTGCTCGCAGAGTTTGCCTCACGACAGAAAAGCTTTATGGAAACTGCAATGGATGTTGATTCTCCTGAGAACGATATTCCTATGGAAATTACCACAGCAGAACCACAAGTTTCTGAGGCCGTGTATGACTGTGTTATTTGTGGACAGAGTGGTCCTTCTTCTGAAGACAGACCTACAGGACTGGTTGTACTGTTACAAGCATCATCAGTTTTAGGCCAGTGCCGGGACAATGCTGAGCCAAAAAAGTTGCCGATCGCTGAAGAGGAGCAGATTTACCCTTGGGACACATGTGCAGCAGTTCATGATGTGAGGCTTTCATTACTGCAGCGTTATTTTAAAGATAGTTCTTGCCTTTTGGCAGTATCAATTGGCTGGGAAGGAGGTGTTTATGTACAAACTTGTGGCCACACGTTGCACATAGATTGTCATAAATCCTATATGGAGTCGTTACGGAATGACCAGGTTCTTCAGGGCTTCTCAGTGGACAAAGGAGAATTCACGTGTCCCCTCTGTAGACAGTTTGCCAACAGTGTTCTTCCATGTTATCCTGGAAGCAATGTGGAAAATAACCTTTGGCAACGCCCTTGTAACAAAAGCACGCAAGATCTCATAAAGGAAGTGGAAGAGCTGCAGGGACGGCCGGGAGCTTTCCCATCAGAAACCAACTTAAGTAAAGAAATGGAATCTGTAATGAAAGATATAAAAAATACCACTCAGAAGAAATACAGAGACTATAGCAAGACCCCAGGCTCACCAGACAACGAGTTTCTCTTTATGTACTCTGTTGCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATAGCAAGACCCCAGGCTCA
60.62
TCAACATCCATTGCAGTTTCCA
58.77
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTCACCAGACAACGAGTT
60.25
CAGGAGAATCAACATCCATTGCA
59.3
142
PCR template sequence:
TGAAAGATATAAAAAATACCACTCAGAAGAAATACAGAGACTATAGCAAGACCCCAGGCTCACCAGACAACGAGTTTCTCTTTATGTACTCTGTTGCTAGGCGACAAAAGGCTAGAGAAAGGCAGCAGAAATTGCTCGCAGAGTTTGCCTCACGACAGAAAAGCTTTATGGAAACTGCAATGGATGTTGATTCTCCTGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-181b-5p(1), mmu-miR-194-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-3470b(1), mmu-miR-1904(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTCTGTTGCTAGGCGACAAAAGGCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUBR3_822_ORF_1
0.8387
0.060355284
0.999625904
1575
ORF sequence:
ATGGAAACTGCAATGGATGTTGATTCTCCTGAGAACGATATTCCTATGGAAATTACCACAGCAGAACCACAAGTTTCTGAGGCCGTGTATGACTGTGTTATTTGTGGACAGAGTGGTCCTTCTTCTGAAGACAGACCTACAGGACTGGTTGTACTGTTACAAGCATCATCAGTTTTAGGCCAGTGCCGGGACAATGCTGAGCCAAAAAAGTTGCCGATCGCTGAAGAGGAGCAGATTTACCCTTGGGACACATGTGCAGCAGTTCATGATGTGAGGCTTTCATTACTGCAGCGTTATTTTAAAGATAGTTCTTGCCTTTTGGCAGTATCAATTGGCTGGGAAGGAGGTGTTTATGTACAAACTTGTGGCCACACGTTGCACATAGATTGTCATAAATCCTATATGGAGTCGTTACGGAATGACCAGGTTCTTCAGGGCTTCTCAGTGGACAAAGGAGAATTCACGTGTCCCCTCTGTAGACAGTTTGCCAACAGTGTTCTTCCATGTTATCCTGGAAGCAATGTGGAAAATAACCTTTGGCAACGCCCTTGTAACAAAAGCACGCAAGATCTCATAAAGGAAGTGGAAGAGCTGCAGGGACGGCCGGGAGCTTTCCCATCAGAAACCAACTTAAGTAAAGAAATGGAATCTGTAATGAAAGATATAAAAAATACCACTCAGAAGAAATACAGAGACTATAGCAAGACCCCAGGCTCACCAGACAACGAGTTTCTCTTTATGTACTCTGTTGCTAGGCGACAAAAGGCTAGAGAAAGGCAGCAGAAATTGCTCGCAGAGTTTGCCTCACGACAGAAAAGCTTTATGGAAACTGCAATGGATGTTGATTCTCCTGAGAACGATATTCCTATGGAAATTACCACAGCAGAACCACAAGTTTCTGAGGCCGTGTATGACTGTGTTATTTGTGGACAGAGTGGTCCTTCTTCTGAAGACAGACCTACAGGACTGGTTGTACTGTTACAAGCATCATCAGTTTTAGGCCAGTGCCGGGACAATGCTGAGCCAAAAAAGTTGCCGATCGCTGAAGAGGAGCAGATTTACCCTTGGGACACATGTGCAGCAGTTCATGATGTGAGGCTTTCATTACTGCAGCGTTATTTTAAAGATAGTTCTTGCCTTTTGGCAGTATCAATTGGCTGGGAAGGAGGTGTTTATGTACAAACTTGTGGCCACACGTTGCACATAGATTGTCATAAATCCTATATGGAGTCGTTACGGAATGACCAGGTTCTTCAGGGCTTCTCAGTGGACAAAGGAGAATTCACGTGTCCCCTCTGTAGACAGTTTGCCAACAGTGTTCTTCCATGTTATCCTGGAAGCAATGTGGAAAATAACCTTTGGCAACGCCCTTGTAACAAAAGCACGCAAGATCTCATAAAGGAAGTGGAAGAGCTGCAGGGACGGCCGGGAGCTTTCCCATCAGAAACCAACTTAAGTAAAGAAATGGAATCTGTAATGAAAGATATAAAAAATACCACTCAGAAGAAATACAGAGACTATAGCAAGACCCCAGGCTCACCAGACAACGAGTTTCTCTTTATGTACTCTGTTGCT
Peptide sequence:
METAMDVDSPENDIPMEITTAEPQVSEAVYDCVICGQSGPSSEDRPTGLVVLLQASSVLGQCRDNAEPKKLPIAEEEQIYPWDTCAAVHDVRLSLLQRYFKDSSCLLAVSIGWEGGVYVQTCGHTLHIDCHKSYMESLRNDQVLQGFSVDKGEFTCPLCRQFANSVLPCYPGSNVENNLWQRPCNKSTQDLIKEVEELQGRPGAFPSETNLSKEMESVMKDIKNTTQKKYRDYSKTPGSPDNEFLFMYSVARRQKARERQQKLLAEFASRQKSFMETAMDVDSPENDIPMEITTAEPQVSEAVYDCVICGQSGPSSEDRPTGLVVLLQASSVLGQCRDNAEPKKLPIAEEEQIYPWDTCAAVHDVRLSLLQRYFKDSSCLLAVSIGWEGGVYVQTCGHTLHIDCHKSYMESLRNDQVLQGFSVDKGEFTCPLCRQFANSVLPCYPGSNVENNLWQRPCNKSTQDLIKEVEELQGRPGAFPSETNLSKEMESVMKDIKNTTQKKYRDYSKTPGSPDNEFLFMYSVA
IRESfinder result
IRESfinder score
0.643255282
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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