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mmu_circAlms1_737

Basic information of circular RNA
PanCircBase ID:

mmu_circAlms1_737

mm39_Chr. Position ID:

chr6|85618300|85644938|+

Gene name:

Alms1

Transcript:

ENSMUST00000072018.6

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

11,12,13,14,15

Exon/intron offsets:

0,1839,9944,15076,26548

Genomic length:

26638

Exon/intron sizes in nt:

230,126,156,135,90

Flanking exon/introns:

chr6:85606696-85618300|chr6:85644938-85654537

Splice length:

737

Other database IDs:

CIRCpedia: MMU_CIRCpedia_32112, circAtlas: mmu-Alms1_0002

Human Ortholog IDs:
Mature spliced Sequence:

TTCACAAGAACAGAGTAAGGTTTCCTTTACTACGTCCTTTGGAAAGTTATCATCTGATGCCATCACTCAGATAACAACAGAAAGTCCAGAAAAGACCACATTTTCATCTGAAATTTTTATTCATGCGGATGATCGTGGACAGGGCATTCTAGACCCCATGGCCCAAAAGCCATCCAGGTTTGCCTCATCATCCTCAGTGCAGCAAATCCCAGCTTCTCATGGCAAAGACGCCCAGCCTGTGCTGTTACCATATAAGCCATCTGGTAGTTCGAAGATGTATTATGTTCCACTGTTAAAAAGAGTTCCTTCATATCTGGATTCCAAATCTGATACCACTGTTGAGAGCTCACATTCAGGCTCAAATGATGCTATTGCCCCAGACTTTCCACCTCAAATGCTAGGCACAAGAGACGATGACCTCTCCAACACTGTAAACATTAAGCACAAAGAAGGGATTTATAGCAAGAGGGCTGCAACAAAGGGGAAAAACCCCTCTCAGAAAGGTGATGCAGCGGCCCCAGTTCAAATGCCTATAACTTGGGATGAGAATGTCTTGGACGAAAACCAAGAAGAGGTCATCAGTAGAGGAGTTGTGATCAAGATGGCAGGACCTGAAGAAATGTCATCCCTGGAGAAGGACCTTGCAGGTCCCAGTGATATCACTGTACAAGACAGAAAAACTGAAAATCTGCCAGACACTAAATCCATTAAACAGAAGGAAGGATCCTTAGAGATAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CCTTGCAGGTCCCAGTGATA

59.09

TCTGAGTGATGGCATCAGATGA

58.96

169

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CCTTGCAGGTCCCAGTGATA

59.09

CTGAGTGATGGCATCAGATGA

57.53

168

PCR template sequence:

GACCTTGCAGGTCCCAGTGATATCACTGTACAAGACAGAAAAACTGAAAATCTGCCAGACACTAAATCCATTAAACAGAAGGAAGGATCCTTAGAGATAGTTCACAAGAACAGAGTAAGGTTTCCTTTACTACGTCCTTTGGAAAGTTATCATCTGATGCCATCACTCAGATAACAACAGAAAGTCCAGAAAAGACCACA

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

6

Interacting miRNAs (#binding sites)

mmu-miR-135a-5p(1), mmu-miR-339-5p(1), mmu-miR-194-5p(1), mmu-miR-218-5p(1), mmu-miR-369-3p(1), mmu-miR-490-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TCCTTAGAGATAGTTCACAAGAACAG

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCALMS1_737_ORF_1

0.9097

0.079829403

0.811535233

654

ORF sequence:

ATGGCCCAAAAGCCATCCAGGTTTGCCTCATCATCCTCAGTGCAGCAAATCCCAGCTTCTCATGGCAAAGACGCCCAGCCTGTGCTGTTACCATATAAGCCATCTGGTAGTTCGAAGATGTATTATGTTCCACTGTTAAAAAGAGTTCCTTCATATCTGGATTCCAAATCTGATACCACTGTTGAGAGCTCACATTCAGGCTCAAATGATGCTATTGCCCCAGACTTTCCACCTCAAATGCTAGGCACAAGAGACGATGACCTCTCCAACACTGTAAACATTAAGCACAAAGAAGGGATTTATAGCAAGAGGGCTGCAACAAAGGGGAAAAACCCCTCTCAGAAAGGTGATGCAGCGGCCCCAGTTCAAATGCCTATAACTTGGGATGAGAATGTCTTGGACGAAAACCAAGAAGAGGTCATCAGTAGAGGAGTTGTGATCAAGATGGCAGGACCTGAAGAAATGTCATCCCTGGAGAAGGACCTTGCAGGTCCCAGTGATATCACTGTACAAGACAGAAAAACTGAAAATCTGCCAGACACTAAATCCATTAAACAGAAGGAAGGATCCTTAGAGATAGTTCACAAGAACAGAGTAAGGTTTCCTTTACTACGTCCTTTGGAAAGTTATCATCTGATGCCATCACTCAGATAA

Peptide sequence:

MAQKPSRFASSSSVQQIPASHGKDAQPVLLPYKPSGSSKMYYVPLLKRVPSYLDSKSDTTVESSHSGSNDAIAPDFPPQMLGTRDDDLSNTVNIKHKEGIYSKRAATKGKNPSQKGDAAAPVQMPITWDENVLDENQEEVISRGVVIKMAGPEEMSSLEKDLAGPSDITVQDRKTENLPDTKSIKQKEGSLEIVHKNRVRFPLLRPLESYHLMPSLR

IRESfinder result

IRESfinder score

0.448183631

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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