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mmu_circFubp3_346

Basic information of circular RNA
PanCircBase ID:

mmu_circFubp3_346

mm39_Chr. Position ID:

chr2|31494625|31498238|+

Gene name:

Fubp3

Transcript:

ENSMUST00000113482.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

10,11,12

Exon/intron offsets:

0,629,3471

Genomic length:

3613

Exon/intron sizes in nt:

10,31,01,142

Flanking exon/introns:

chr2:31493327-31494625|chr2:31498238-31501590

Splice length:

346

Other database IDs:

circAtlas: mmu-Fubp3_0018

circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_63163

Human Ortholog IDs:
Mature spliced Sequence:

GTGTCTGTGCCTAGGTTTGTTGTTGGGATTGTCATAGGAAGGAACGGAGAAATGATTAAGAAGATCCAGAACGACGCTGGTGTGAGGATCCAATTCAAACCAGATGACGGGATTAGTCCAGAAAGAGCAGCGCAGGTCATGGGCCCTCCAGATCGGTGTCAGCATGCAGCTCGCATCATCAATGAGCTCATTCTCACGGCACAGGAAAGAGAGATCCTTGGTGGCCTCACAGTAACAAGAGGAAGAGGCCGAGGCCGTAGTGACTGGAGTGTGGGCACTCCTGGGGGCGTCCAGGAAATTACGTACACAGTGCCAGCTGATAAGTGCGGCCTTGTGATAGGCAAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TACGTACACAGTGCCAGCTG

60.04

ATTGGATCCTCACACCAGCG

60.11

141

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGGCGTCCAGGAAATTACGT

60.39

ATTGGATCCTCACACCAGCG

60.11

156

PCR template sequence:

GGCCGAGGCCGTAGTGACTGGAGTGTGGGCACTCCTGGGGGCGTCCAGGAAATTACGTACACAGTGCCAGCTGATAAGTGCGGCCTTGTGATAGGCAAAGGTGTCTGTGCCTAGGTTTGTTGTTGGGATTGTCATAGGAAGGAACGGAGAAATGATTAAGAAGATCCAGAACGACGCTGGTGTGAGGATCCAATTCAAAC

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-495-3p(1), mmu-miR-29b-1-5p(1)

siRNAs for circular RNA silencing
Junction sequence

GTGATAGGCAAAGGTGTCTGTGCCTA

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCFUBP3_346_ORF_1

0.9829

0.276029121

0.481745803

309

ORF sequence:

ATGATTAAGAAGATCCAGAACGACGCTGGTGTGAGGATCCAATTCAAACCAGATGACGGGATTAGTCCAGAAAGAGCAGCGCAGGTCATGGGCCCTCCAGATCGGTGTCAGCATGCAGCTCGCATCATCAATGAGCTCATTCTCACGGCACAGGAAAGAGAGATCCTTGGTGGCCTCACAGTAACAAGAGGAAGAGGCCGAGGCCGTAGTGACTGGAGTGTGGGCACTCCTGGGGGCGTCCAGGAAATTACGTACACAGTGCCAGCTGATAAGTGCGGCCTTGTGATAGGCAAAGGTGTCTGTGCCTAG

Peptide sequence:

MIKKIQNDAGVRIQFKPDDGISPERAAQVMGPPDRCQHAARIINELILTAQEREILGGLTVTRGRGRGRSDWSVGTPGGVQEITYTVPADKCGLVIGKGVCA

IRESfinder result

IRESfinder score

0.342565482

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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