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mmu_circPolr2b_819

Basic information of circular RNA
PanCircBase ID:

mmu_circPolr2b_819

mm39_Chr. Position ID:

chr5|77488221|77493258|+

Gene name:

Polr2b

Transcript:

ENSMUST00000031167.6

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

6

Exon/intron indexes:

18,19,20,21,22,23

Exon/intron offsets:

0,2155,2486,2795,4417,4876

Genomic length:

5037

Exon/intron sizes in nt:

9,52,51,90,10,81,14,160

Flanking exon/introns:

chr5:77487264-77488221|chr5:77493258-77496069

Splice length:

819

Other database IDs:

circBase: hsa_circ_0126704, circAtlas: hsa-POLR2B_0012, CIRCpedia: HSA_CIRCpedia_137408

Human Ortholog IDs:
Mature spliced Sequence:

GTCTGTTTTCTACCGATCATACAAAGAACAAGAGTCTAAAAAGGGATTTGATCAAGAAGAAGTGTTTGAGAAGCCTACACGTGAGACATGCCAGGGAATGAGGCATGCCATCTATGAAAAGTTGGACGATGACGGTTTGATAGCTCCGGGGGTCCGAGTCTCCGGAGATGACGTTATTATCGGCAAGACAGTCACCTTACCCGAGAACGAGGATGAGCTGGAGAGCACCAACAGGCGCTACACCAAGAGGGACTGCAGCACTTTCCTCAGAACTAGTGAGACGGGCATCGTGGACCAGGTCATGGTCACTCTCAACCAGGAAGGATATAAATTTTGTAAAATAAGGGTGCGCTCTGTTAGAATTCCGCAGATTGGAGACAAATTTGCTAGCCGACATGGTCAGAAGGGAACTTGTGGTATTCAGTATAGACAAGAGGACATGCCGTTCACTTGCGAAGGCATAACTCCTGACATCATCATAAACCCCCACGCCATCCCCTCCCGGATGACAATTGGTCACTTGATCGAATGTCTCCAAGGGAAGGTCTCTGCCAACAAGGGTGAAATTGGTGACGCTACTCCATTTAATGATGCTGTCAATGTGCAGAAGATTTCTAATCTTTTGTCTGACTATGGCTACCATCTCAGAGGGAACGAGGTGCTCTACAATGGATTCACTGGACGAAAAATCACATCACAGATTTTTATTGGCCCCACTTACTACCAGCGTTTGAAGCATATGGTGGATGACAAAATTCATTCTCGTGCTAGGGGACCCATTCAGATTCTTAACAGACAGCCCATGGAGGGCAGATCTCG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCATTCTCGTGCTAGGGGAC

58.89

ATTCCCTGGCATGTCTCACG

60.11

162

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCATTCTCGTGCTAGGGGAC

58.89

GCATGTCTCACGTGTAGGCT

60.11

154

PCR template sequence:

ACTACCAGCGTTTGAAGCATATGGTGGATGACAAAATTCATTCTCGTGCTAGGGGACCCATTCAGATTCTTAACAGACAGCCCATGGAGGGCAGATCTCGGTCTGTTTTCTACCGATCATACAAAGAACAAGAGTCTAAAAAGGGATTTGATCAAGAAGAAGTGTTTGAGAAGCCTACACGTGAGACATGCCAGGGAATG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

10

Interacting miRNAs (#binding sites)

mmu-miR-20b-5p(1), mmu-miR-134-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-211-5p(1), mmu-miR-106b-5p(1), mmu-miR-431-5p(1), mmu-miR-532-5p(1)

siRNAs for circular RNA silencing
Junction sequence

AGGGCAGATCTCGGTCTGTTTTCTAC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCPOLR2B_819_ORF_1

1.1857

0.271857565

0.999892835

1539

ORF sequence:

ATGAGGCATGCCATCTATGAAAAGTTGGACGATGACGGTTTGATAGCTCCGGGGGTCCGAGTCTCCGGAGATGACGTTATTATCGGCAAGACAGTCACCTTACCCGAGAACGAGGATGAGCTGGAGAGCACCAACAGGCGCTACACCAAGAGGGACTGCAGCACTTTCCTCAGAACTAGTGAGACGGGCATCGTGGACCAGGTCATGGTCACTCTCAACCAGGAAGGATATAAATTTTGTAAAATAAGGGTGCGCTCTGTTAGAATTCCGCAGATTGGAGACAAATTTGCTAGCCGACATGGTCAGAAGGGAACTTGTGGTATTCAGTATAGACAAGAGGACATGCCGTTCACTTGCGAAGGCATAACTCCTGACATCATCATAAACCCCCACGCCATCCCCTCCCGGATGACAATTGGTCACTTGATCGAATGTCTCCAAGGGAAGGTCTCTGCCAACAAGGGTGAAATTGGTGACGCTACTCCATTTAATGATGCTGTCAATGTGCAGAAGATTTCTAATCTTTTGTCTGACTATGGCTACCATCTCAGAGGGAACGAGGTGCTCTACAATGGATTCACTGGACGAAAAATCACATCACAGATTTTTATTGGCCCCACTTACTACCAGCGTTTGAAGCATATGGTGGATGACAAAATTCATTCTCGTGCTAGGGGACCCATTCAGATTCTTAACAGACAGCCCATGGAGGGCAGATCTCGGTCTGTTTTCTACCGATCATACAAAGAACAAGAGTCTAAAAAGGGATTTGATCAAGAAGAAGTGTTTGAGAAGCCTACACGTGAGACATGCCAGGGAATGAGGCATGCCATCTATGAAAAGTTGGACGATGACGGTTTGATAGCTCCGGGGGTCCGAGTCTCCGGAGATGACGTTATTATCGGCAAGACAGTCACCTTACCCGAGAACGAGGATGAGCTGGAGAGCACCAACAGGCGCTACACCAAGAGGGACTGCAGCACTTTCCTCAGAACTAGTGAGACGGGCATCGTGGACCAGGTCATGGTCACTCTCAACCAGGAAGGATATAAATTTTGTAAAATAAGGGTGCGCTCTGTTAGAATTCCGCAGATTGGAGACAAATTTGCTAGCCGACATGGTCAGAAGGGAACTTGTGGTATTCAGTATAGACAAGAGGACATGCCGTTCACTTGCGAAGGCATAACTCCTGACATCATCATAAACCCCCACGCCATCCCCTCCCGGATGACAATTGGTCACTTGATCGAATGTCTCCAAGGGAAGGTCTCTGCCAACAAGGGTGAAATTGGTGACGCTACTCCATTTAATGATGCTGTCAATGTGCAGAAGATTTCTAATCTTTTGTCTGACTATGGCTACCATCTCAGAGGGAACGAGGTGCTCTACAATGGATTCACTGGACGAAAAATCACATCACAGATTTTTATTGGCCCCACTTACTACCAGCGTTTGAAGCATATGGTGGATGACAAAATTCATTCTCGTGCTAGGGGACCCATTCAGATTCTTAACAGACAGCCCATGGAGGGCAGATCT

Peptide sequence:

MRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYEKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRS

IRESfinder result

IRESfinder score

0.424785506

IRES/non IRES

non-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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