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mmu_circAlpk1_386

Basic information of circular RNA
PanCircBase ID:

mmu_circAlpk1_386

mm39_Chr. Position ID:

chr3|127518023|127523150|-

Gene name:

Alpk1

Transcript:

ENSMUST00000029662.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

3,2

Exon/intron offsets:

0,4896

Genomic length:

5127

Exon/intron sizes in nt:

155,231

Flanking exon/introns:

chr3:127489401-127518023|chr3:127523150-127573809

Splice length:

386

Other database IDs:

CIRCpedia: MMU_CIRCpedia_220024, circAtlas: mmu-Alpk1_0001

Human Ortholog IDs:
Mature spliced Sequence:

GTACCTCAGCCTTCAAGGGCCTTCTTTATTGAGAATCAATGCCTCTCCTAGGTAATTGATCACCATAGACCCAGGGAGACTCAATTCATCCTGGAGGGTGGGTAATCGTCATGAATAATCAAGATGCCGTGGCTTCGATACTGCATGAGTGCAAGCAAGTGCTGGATCGTCTCTTGTTGGAAACGCCAGATGTGTCTACAGAGGACAAGAGTGAGGACCAGCGGTGCAGAGCTTCACTCCCCAGCGAGTTAAGGACCCTGATCCAGGAGGCAGAGGAAATGAAGTGGCCCTTCGTGCCTGAAAAGTGGCAATACAAACAAGCCATGAGCCCAGAGGACAAAACAAACCTGCAAGATGTGATTGGCGCCGGGCTGCAGCAGTTACTG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AAACAAGCCATGAGCCCAGA

59.89

TCTCCCTGGGTCTATGGTGA

58.98

151

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AAACAAGCCATGAGCCCAGA

59.89

AGTCTCCCTGGGTCTATGGT

58.98

153

PCR template sequence:

GCCCTTCGTGCCTGAAAAGTGGCAATACAAACAAGCCATGAGCCCAGAGGACAAAACAAACCTGCAAGATGTGATTGGCGCCGGGCTGCAGCAGTTACTGGTACCTCAGCCTTCAAGGGCCTTCTTTATTGAGAATCAATGCCTCTCCTAGGTAATTGATCACCATAGACCCAGGGAGACTCAATTCATCCTGGAGGGTG

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

3

Interacting miRNAs (#binding sites)

mmu-miR-135a-5p(1), mmu-miR-127-5p(1), mmu-miR-5101(1)

siRNAs for circular RNA silencing
Junction sequence

GCAGCAGTTACTGGTACCTCAGCCTT

siRNA sets

CTGAGGTACCAGTAACTGC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCALPK1_386_ORF_1

1.0259

0.247421086

0.504494836

327

ORF sequence:

ATGAATAATCAAGATGCCGTGGCTTCGATACTGCATGAGTGCAAGCAAGTGCTGGATCGTCTCTTGTTGGAAACGCCAGATGTGTCTACAGAGGACAAGAGTGAGGACCAGCGGTGCAGAGCTTCACTCCCCAGCGAGTTAAGGACCCTGATCCAGGAGGCAGAGGAAATGAAGTGGCCCTTCGTGCCTGAAAAGTGGCAATACAAACAAGCCATGAGCCCAGAGGACAAAACAAACCTGCAAGATGTGATTGGCGCCGGGCTGCAGCAGTTACTGGTACCTCAGCCTTCAAGGGCCTTCTTTATTGAGAATCAATGCCTCTCCTAG

Peptide sequence:

MNNQDAVASILHECKQVLDRLLLETPDVSTEDKSEDQRCRASLPSELRTLIQEAEEMKWPFVPEKWQYKQAMSPEDKTNLQDVIGAGLQQLLVPQPSRAFFIENQCLS

IRESfinder result

IRESfinder score

0.472879988

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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