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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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Institute of Life sciences, Bhubaneswar, India

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