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mmu_circTenm3_477

Basic information of circular RNA
PanCircBase ID:

mmu_circTenm3_477

mm39_Chr. Position ID:

chr8|48848470|48870280|-

Gene name:

Tenm3

Transcript:

ENSMUST00000033965.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

4,3

Exon/intron offsets:

0,21572

Genomic length:

21810

Exon/intron sizes in nt:

239,238

Flanking exon/introns:

chr8:48820468-48848470|chr8:48870280-49099292

Splice length:

477

Other database IDs:

circBase: mmu_circ_0014854, CIRCpedia: MMU_CIRCpedia_21325, circAtlas: mmu-Tenm3_0007

circBase: hsa_circ_0071480, circAtlas: hsa-TENM3_0003, CIRCpedia: HSA_CIRCpedia_48013

Human Ortholog IDs:
Mature spliced Sequence:

AGCAACCTTCAAACAACCCAGGGCAACCCACCCTGCAGCCTTTGCCGCCATCCCACAAGCAGCACCCGGCGCAGCATCACCCGTCCATCACTTCCCTCAATAGAAACTCCCTGACCAATAGAAGGAACCAGAGTCCGGCCCCGCCGGCTGCTTTGCCCGCCGAGCTGCAAACCACACCCGAGTCCGTCCAGCTGCAGGACAGCTGGGTCCTTGGCAGTAATGTACCACTGGAAAGCAGGCATTTCCTATTCAAAACAGGGACAGGGACGACGCCACTGTTCAGTACGGCAACCCCGGGATACACAATGGCATCTGGCTCTGTTTATTCTCCGCCTACCCGGCCACTTCCTAGAAACACCCTATCAAGAAGTGCTTTTAAATTCAAGAAGTCTTCAAAGTACTGCAGCTGGAGGTGCACCGCACTGTGTGCTGTAGGGGTCTCAGTGCTCCTGGCCATTCTCCTCTCCTATTTTATAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGTGCTGTAGGGGTCTCAGT

60.18

AAGTGATGGACGGGTGATGC

60.39

145

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTGCTGTAGGGGTCTCAGTG

59.75

AAGTGATGGACGGGTGATGC

60.39

144

PCR template sequence:

AAATTCAAGAAGTCTTCAAAGTACTGCAGCTGGAGGTGCACCGCACTGTGTGCTGTAGGGGTCTCAGTGCTCCTGGCCATTCTCCTCTCCTATTTTATAGAGCAACCTTCAAACAACCCAGGGCAACCCACCCTGCAGCCTTTGCCGCCATCCCACAAGCAGCACCCGGCGCAGCATCACCCGTCCATCACTTCCCTCAA

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-29b-1-5p(1), mmu-miR-666-5p(1)

siRNAs for circular RNA silencing
Junction sequence

TCCTATTTTATAGAGCAACCTTCAAA

siRNA sets

TTTGAAGGTTGCTCTATAA, GTTGCTCTATAAAATAGGA, GGTTGCTCTATAAAATAGG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCTENM3_477_ORF_1

0.6853

0.020022253

0.682876364

648

ORF sequence:

ATGGCATCTGGCTCTGTTTATTCTCCGCCTACCCGGCCACTTCCTAGAAACACCCTATCAAGAAGTGCTTTTAAATTCAAGAAGTCTTCAAAGTACTGCAGCTGGAGGTGCACCGCACTGTGTGCTGTAGGGGTCTCAGTGCTCCTGGCCATTCTCCTCTCCTATTTTATAGAGCAACCTTCAAACAACCCAGGGCAACCCACCCTGCAGCCTTTGCCGCCATCCCACAAGCAGCACCCGGCGCAGCATCACCCGTCCATCACTTCCCTCAATAGAAACTCCCTGACCAATAGAAGGAACCAGAGTCCGGCCCCGCCGGCTGCTTTGCCCGCCGAGCTGCAAACCACACCCGAGTCCGTCCAGCTGCAGGACAGCTGGGTCCTTGGCAGTAATGTACCACTGGAAAGCAGGCATTTCCTATTCAAAACAGGGACAGGGACGACGCCACTGTTCAGTACGGCAACCCCGGGATACACAATGGCATCTGGCTCTGTTTATTCTCCGCCTACCCGGCCACTTCCTAGAAACACCCTATCAAGAAGTGCTTTTAAATTCAAGAAGTCTTCAAAGTACTGCAGCTGGAGGTGCACCGCACTGTGTGCTGTAGGGGTCTCAGTGCTCCTGGCCATTCTCCTCTCCTATTTTATA

Peptide sequence:

MASGSVYSPPTRPLPRNTLSRSAFKFKKSSKYCSWRCTALCAVGVSVLLAILLSYFIEQPSNNPGQPTLQPLPPSHKQHPAQHHPSITSLNRNSLTNRRNQSPAPPAALPAELQTTPESVQLQDSWVLGSNVPLESRHFLFKTGTGTTPLFSTATPGYTMASGSVYSPPTRPLPRNTLSRSAFKFKKSSKYCSWRCTALCAVGVSVLLAILLSYFI

IRESfinder result

IRESfinder score

0.487088604

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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