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mmu_circSmarcb1_396

Basic information of circular RNA
PanCircBase ID:

mmu_circSmarcb1_396

mm39_Chr. Position ID:

chr10|75745987|75751027|-

Gene name:

Smarcb1

Transcript:

ENSMUST00000000925.10

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

5,4,3

Exon/intron offsets:

0,1365,4910

Genomic length:

5040

Exon/intron sizes in nt:

12,81,38,130

Flanking exon/introns:

chr10:75742030-75745987|chr10:75751027-75752606

Splice length:

396

Other database IDs:

circAtlas: hsa-SMARCB1_0007, CIRCpedia: HSA_CIRCpedia_365119

Human Ortholog IDs:
Mature spliced Sequence:

ATCATGGATATACCACCCTGGCCACCAGCGTGACACTCCTGAAAGCCTCAGAGGTAGAAGAGATCCTGGATGGCAATGACGAGAAGTACAAGGCTGTGTCCATCAGCACAGAGCCCCCGACCTACCTCAGGGAGCAGAAGGCCAAGAGGAACAGCCAGTGGGTCCCCACCCTGCCCAACAGCTCCCACCACCTGGATGCTGTGCCCTGTTCCACCACCATCAACAGGAACCGCATGGGTCGGGACAAGAAGAGAACCTTCCCCTTGTGCTTTGATGACCACGACCCAGCTGTGATCCATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAATG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CTCGACATGGAGATCGACGG

60.04

CTCGTCATTGCCATCCAGGA

59.82

141

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CTCGACATGGAGATCGACGG

60.04

TCTCGTCATTGCCATCCAGG

59.82

142

PCR template sequence:

CATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAATGATCATGGATATACCACCCTGGCCACCAGCGTGACACTCCTGAAAGCCTCAGAGGTAGAAGAGATCCTGGATGGCAATGACGAGAAGTACAAGGCTGTGTC

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

5

Interacting miRNAs (#binding sites)

mmu-miR-122-5p(1), mmu-miR-705(1), mmu-miR-673-5p(1), mmu-miR-670-5p(1), mmu-miR-1904(1)

siRNAs for circular RNA silencing
Junction sequence

TGGAACATGAATGATCATGGATATAC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCSMARCB1_396_ORF_1

1.3113

0.59304934

0.974127392

558

ORF sequence:

ATGGGTCGGGACAAGAAGAGAACCTTCCCCTTGTGCTTTGATGACCACGACCCAGCTGTGATCCATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAATGATCATGGATATACCACCCTGGCCACCAGCGTGACACTCCTGAAAGCCTCAGAGGTAGAAGAGATCCTGGATGGCAATGACGAGAAGTACAAGGCTGTGTCCATCAGCACAGAGCCCCCGACCTACCTCAGGGAGCAGAAGGCCAAGAGGAACAGCCAGTGGGTCCCCACCCTGCCCAACAGCTCCCACCACCTGGATGCTGTGCCCTGTTCCACCACCATCAACAGGAACCGCATGGGTCGGGACAAGAAGAGAACCTTCCCCTTGTGCTTTGATGACCACGACCCAGCTGTGATCCATGAGAATGCGTCACAGCCTGAGGTGCTGGTGCCCATCCGGCTCGACATGGAGATCGACGGGCAGAAGCTGCGAGACGCTTTTACCTGGAACATGAAT

Peptide sequence:

MGRDKKRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLRDAFTWNMNDHGYTTLATSVTLLKASEVEEILDGNDEKYKAVSISTEPPTYLREQKAKRNSQWVPTLPNSSHHLDAVPCSTTINRNRMGRDKKRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLRDAFTWNMN

IRESfinder result

IRESfinder score

0.272540827

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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