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mmu_circSbno1_496

Basic information of circular RNA
PanCircBase ID:

mmu_circSbno1_496

mm39_Chr. Position ID:

chr5|124522529|124526723|-

Gene name:

Sbno1

Transcript:

ENSMUST00000065263.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

25,24,23,22,21

Exon/intron offsets:

0,2363,2852,3010,4058

Genomic length:

4194

Exon/intron sizes in nt:

75,10,07,21,13,136

Flanking exon/introns:

chr5:124520068-124522529|chr5:124526723-124529984

Splice length:

496

Other database IDs:

circAtlas: mmu-Sbno1_0047

Human Ortholog IDs:
Mature spliced Sequence:

AATATTGCTATTATCTCAGAAGCTGCCAGCTCAGGTATTTCATTACAAGCAGATCGGAGAGCTAAAAACCAAAGGCGAAGAGTTCACATGACTTTAGAATTACCTTGGAGTGCTGATAGGGCGATTCAGCAGTTTGGAAGAACACACAGGTCAAACCAAGTGACTGCTCCAGAGTATGTTTTTTTGATTTCGGAACTGGCTGGAGAACAGAGATTTGCATCTATTGTTGCTAAAAGACTTGAGAGTTTGGGGGCACTTACACATGGTGACAGAAGAGCAACAGAATCTAGAGATCTGAGCAGATTCAACTTTGACAACAAGTATGGAAGAAATGCTTTAGAAATTGTTATGAAATCCATTGTAAACTTGGATTCTCCTATGGTATCACCACCTCCAGACTACCCTGGAGAATTCTTTAAAGACGTTCGGCAAGGACTGATAGGAGTGGGCTTGATTAATGTAGAGGATCGCTCAGGAATTCTTACTCTTGATAAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AAAGACGTTCGGCAAGGACT

59.89

TGTGAACTCTTCGCCTTTGGT

60.13

167

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GACGTTCGGCAAGGACTGAT

60.39

TGTGAACTCTTCGCCTTTGGT

60.13

164

PCR template sequence:

GACTACCCTGGAGAATTCTTTAAAGACGTTCGGCAAGGACTGATAGGAGTGGGCTTGATTAATGTAGAGGATCGCTCAGGAATTCTTACTCTTGATAAAGAATATTGCTATTATCTCAGAAGCTGCCAGCTCAGGTATTTCATTACAAGCAGATCGGAGAGCTAAAAACCAAAGGCGAAGAGTTCACATGACTTTAGAAT

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

2

Interacting miRNAs (#binding sites)

mmu-miR-9-5p(1), mmu-miR-467b-5p(1)

siRNAs for circular RNA silencing
Junction sequence

ACTCTTGATAAAGAATATTGCTATTA

siRNA sets

ATAGCAATATTCTTTATCA,AATAGCAATATTCTTTATC,TAATAGCAATATTCTTTAT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSBNO1_496_ORF_1

0.6983

-0.064659944

0.307559286

474

ORF sequence:

ATGACTTTAGAATTACCTTGGAGTGCTGATAGGGCGATTCAGCAGTTTGGAAGAACACACAGGTCAAACCAAGTGACTGCTCCAGAGTATGTTTTTTTGATTTCGGAACTGGCTGGAGAACAGAGATTTGCATCTATTGTTGCTAAAAGACTTGAGAGTTTGGGGGCACTTACACATGGTGACAGAAGAGCAACAGAATCTAGAGATCTGAGCAGATTCAACTTTGACAACAAGTATGGAAGAAATGCTTTAGAAATTGTTATGAAATCCATTGTAAACTTGGATTCTCCTATGGTATCACCACCTCCAGACTACCCTGGAGAATTCTTTAAAGACGTTCGGCAAGGACTGATAGGAGTGGGCTTGATTAATGTAGAGGATCGCTCAGGAATTCTTACTCTTGATAAAGAATATTGCTATTATCTCAGAAGCTGCCAGCTCAGGTATTTCATTACAAGCAGATCGGAGAGCTAA

Peptide sequence:

MTLELPWSADRAIQQFGRTHRSNQVTAPEYVFLISELAGEQRFASIVAKRLESLGALTHGDRRATESRDLSRFNFDNKYGRNALEIVMKSIVNLDSPMVSPPPDYPGEFFKDVRQGLIGVGLINVEDRSGILTLDKEYCYYLRSCQLRYFITSRSES

IRESfinder result

IRESfinder score

0.726364329

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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