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mmu_circRap1a_611

Basic information of circular RNA
PanCircBase ID:

mmu_circRap1a_611

mm39_Chr. Position ID:

chr3|105639271|105657644|-

Gene name:

Rap1a

Transcript:

ENSMUST00000090678.11

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

6

Exon/intron indexes:

7,6,5,4,3,2

Exon/intron offsets:

0,5799,7558,9390,13948,18289

Genomic length:

18373

Exon/intron sizes in nt:

116,144,141,57,69,84

Flanking exon/introns:

chr3:105636280-105639271|chr3:105657644-105708554

Splice length:

611

Other database IDs:

circBase: hsa_circ_0110426, circAtlas: hsa-RAP1A_0001, CIRCpedia: HSA_CIRCpedia_27288

Human Ortholog IDs:
Mature spliced Sequence:

ATTGTCAATATTTAAACAGAGCGCATCATGCGTGAGTACAAGCTAGTAGTCCTTGGTTCAGGAGGCGTGGGGAAGTCTGCTCTGACAGTTCAGTTTGTTCAGGGGATTTTTGTTGAAAAATATGACCCAACGATAGAAGATTCCTACAGAAAGCAAGTCGAGGTAGATTGCCAACAGTGCATGCTGGAGATCCTGGACACTGCAGGAACCGAGCAATTTACAGCAATGAGGGATTTGTATATGAAGAATGGCCAAGGGTTTGCACTAGTTTATTCAATTACAGCTCAGTCTACGTTTAATGATTTACAAGACTTGAGAGAACAGATTTTACGGGTTAAAGACACAGAAGATGTTCCAATGATTTTGGTTGGCAATAAATGTGACTTGGAAGATGAACGGGTAGTTGGCAAAGAACAAGGCCAGAATTTAGCAAGACAGTGGTGTAACTGTGCCTTTTTAGAATCTTCTGCAAAGTCAAAGATCAACGTTAATGAGATATTTTATGACCTGGTCAGACAGATAAATAGAAAAACACCAGTGGAAAAGAAGAAGCCTAAAAAGAAATCATGTTTGCTGCTCTAGACCTGAAGTCAGCAGCAGCTCTGAGCCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACCAGTGGAAAAGAAGAAGCCT

59.82

GTCAGAGCAGACTTCCCCAC

60.04

164

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CACCAGTGGAAAAGAAGAAGCC

59.71

GTCAGAGCAGACTTCCCCAC

60.04

165

PCR template sequence:

TCAGACAGATAAATAGAAAAACACCAGTGGAAAAGAAGAAGCCTAAAAAGAAATCATGTTTGCTGCTCTAGACCTGAAGTCAGCAGCAGCTCTGAGCCAGATTGTCAATATTTAAACAGAGCGCATCATGCGTGAGTACAAGCTAGTAGTCCTTGGTTCAGGAGGCGTGGGGAAGTCTGCTCTGACAGTTCAGTTTGTTC

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

9

Interacting miRNAs (#binding sites)

mmu-miR-15a-5p(1), mmu-miR-19b-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-19a-3p(1), mmu-miR-301a-3p(1), mmu-miR-3065-5p(1), mmu-miR-99a-5p(1), mmu-miR-338-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AGCTCTGAGCCAGATTGTCAATATTT

siRNA sets

AAATATTGACAATCTGGCT, ATATTGACAATCTGGCTCA, AATATTGACAATCTGGCTC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

NA

NA

NA

NA

NA

ORF sequence:

NA

Peptide sequence:

NA

IRESfinder result

IRESfinder score

0.634174553

IRES/non IRES

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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