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mmu_circLdlrad3_261

Basic information of circular RNA
PanCircBase ID:

mmu_circLdlrad3_261

mm39_Chr. Position ID:

chr2|101888251|101900403|-

Gene name:

Ldlrad3

Transcript:

ENSMUST00000111222.2

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

4,3

Exon/intron offsets:

0,12026

Genomic length:

12152

Exon/intron sizes in nt:

1,35,126

Flanking exon/introns:

chr2:101785519-101888251|chr2:101900403-101943973

Splice length:

261

Other database IDs:

CIRCpedia: MMU_CIRCpedia_635, circAtlas: mmu-Ldlrad3_0001

circBase: hsa_circ_0004453, circAtlas: hsa-LDLRAD3_0001, CIRCpedia: HSA_CIRCpedia_4252

Human Ortholog IDs:
Mature spliced Sequence:

CCAAAGCAAAATCAAAATGTGGCCCGACCTTCTTCCCCTGCGCCAGTGGCATCCACTGTATCATCGGCCGCTTCCGCTGCAATGGATTTGAGGACTGTCCCGACGGCAGCGACGAGGAGAACTGCACAGCGAACCCCCTGCTTTGCTCCACGGCTCGCTACCACTGCAGGAACGGCCTGTGCATCGACAAGAGCTTCATCTGCGATGGTCAGAATAACTGTCAAGACAACAGTGACGAGGAGAGCTGCGAGAGTTCTCTAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CCTGTGCATCGACAAGAGCT

60.39

CCTCAAATCCATTGCAGCGG

59.9

179

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGCTTCATCTGCGATGGTCA

59.46

CCTCAAATCCATTGCAGCGG

59.9

163

PCR template sequence:

CACTGCAGGAACGGCCTGTGCATCGACAAGAGCTTCATCTGCGATGGTCAGAATAACTGTCAAGACAACAGTGACGAGGAGAGCTGCGAGAGTTCTCTAGCCAAAGCAAAATCAAAATGTGGCCCGACCTTCTTCCCCTGCGCCAGTGGCATCCACTGTATCATCGGCCGCTTCCGCTGCAATGGATTTGAGGACTGTCC

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

NA

Interacting miRNAs (#binding sites)

NA

siRNAs for circular RNA silencing
Junction sequence

GAGAGTTCTCTAGCCAAAGCAAAATC

siRNA sets

ATTTTGCTTTGGCTAGAGA,TTTGCTTTGGCTAGAGAAC,GATTTTGCTTTGGCTAGAG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCLDLRAD3_261_ORF_1

1.02

-0.069920743

0.087431527

180

ORF sequence:

ATGGATTTGAGGACTGTCCCGACGGCAGCGACGAGGAGAACTGCACAGCGAACCCCCTGCTTTGCTCCACGGCTCGCTACCACTGCAGGAACGGCCTGTGCATCGACAAGAGCTTCATCTGCGATGGTCAGAATAACTGTCAAGACAACAGTGACGAGGAGAGCTGCGAGAGTTCTCTAG

Peptide sequence:

MDLRTVPTAATRRTAQRTPCFAPRLATTAGTACASTRASSAMVRITVKTTVTRRAARVL

IRESfinder result

IRESfinder score

0.403279365

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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