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mmu_circAbca5_416

Basic information of circular RNA
PanCircBase ID:

mmu_circAbca5_416

mm39_Chr. Position ID:

chr11|110176519|110179002|-

Gene name:

Abca5

Transcript:

ENSMUST00000043961.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

28,27,26,25

Exon/intron offsets:

0,1070,1888,2369

Genomic length:

2483

Exon/intron sizes in nt:

9,27,51,35,114

Flanking exon/introns:

chr11:110170578-110176519|chr11:110179002-110180616

Splice length:

416

Other database IDs:

circBase: hsa_circ_0107589, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_22233

Human Ortholog IDs:
Mature spliced Sequence:

GTGTTTTGCCTCATTGCTTATGTGCCCTCCGTCATTCTGTTCACGTACATAGCTTCGTTCACTTTCAAGAAAATTTTAAATACCAAGGAATTTTGGTCATTTATCTATTCTGTGACCGCATTGGCTTGTGTGGCAATCACGGAAACAACTTTCTTTCTGCAATATGCAGTTACGGCTGTCTTTCATTACACCTTCTGCATAGCCATTCCAATCTACCCTCTCCTGGGTTGTCTGATTTCTTTCATAAAGGGTTCTTGGAAGAATATGCCAAAAAATGAGAATACCTACAATCCCTGGGATAGACTTTTAGTTGCTGTAATCATGCCCTACCTGCAGTGTATACTGTGGATTTTCCTCTTACAACACTATGAGAAAATACATGGAGGCAGATCTATAAGAAAGGATCCATTTTTCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ATCATGCCCTACCTGCAGTG

59.82

GAACAGAATGACGGAGGGCA

60.04

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ATCATGCCCTACCTGCAGTG

59.82

TGAACAGAATGACGGAGGGC

60.04

141

PCR template sequence:

TAATCATGCCCTACCTGCAGTGTATACTGTGGATTTTCCTCTTACAACACTATGAGAAAATACATGGAGGCAGATCTATAAGAAAGGATCCATTTTTCAGGTGTTTTGCCTCATTGCTTATGTGCCCTCCGTCATTCTGTTCACGTACATAGCTTCGTTCACTTTCAAGAAAATTTTAAATACCAAGGAATTTTGGTCAT

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-382-5p(1), mmu-miR-541-5p(1), mmu-miR-802-5p(1)

siRNAs for circular RNA silencing
Junction sequence

ATCCATTTTTCAGGTGTTTTGCCTCA

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCABCA5_416_ORF_1

0.4192

-0.285848254

0.015073811

204

ORF sequence:

ATGCCAAAAAATGAGAATACCTACAATCCCTGGGATAGACTTTTAGTTGCTGTAATCATGCCCTACCTGCAGTGTATACTGTGGATTTTCCTCTTACAACACTATGAGAAAATACATGGAGGCAGATCTATAAGAAAGGATCCATTTTTCAGGTGTTTTGCCTCATTGCTTATGTGCCCTCCGTCATTCTGTTCACGTACATAG

Peptide sequence:

MPKNENTYNPWDRLLVAVIMPYLQCILWIFLLQHYEKIHGGRSIRKDPFFRCFASLLMCPPSFCSRT

IRESfinder result

IRESfinder score

0.865158466

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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