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mmu_circAtg4b_273

Basic information of circular RNA
PanCircBase ID:

mmu_circAtg4b_273

mm39_Chr. Position ID:

chr1|93695774|93701590|+

Gene name:

Atg4b

Transcript:

ENSMUST00000149436.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

2,3,4

Exon/intron offsets:

0,200,5717

Genomic length:

5816

Exon/intron sizes in nt:

102,72,99

Flanking exon/introns:

chr1:93679303-93695774|chr1:93701590-93702854

Splice length:

273

Other database IDs:

CIRCpedia: MMU_CIRCpedia_215553, circAtlas: mmu-Atg4b_0001

Human Ortholog IDs:
Mature spliced Sequence:

CCACTTTGACATATGATACTCTCCGGTTTGCTGAATTTGAAGATTTCCCTGAGACCTCAGAGCCTGTTTGGATTCTGGGCAGAAAATACAGCATTTTCACAGAGAAGGACGAAATCTTGTCTGATGTTGCATCCAGACTTTGGTTTACATACAGGAGAAACTTTCCAGCTATTGGGGGAACTGGCCCTACTTCAGACACAGGCTGGGGTTGCATGCTTCGGTGTGGACAGATGATCTTTGCCCAGGCCCTGGTATGCCGGCACTTAGGTCGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGCCCTACTTCAGACACAGG

59.75

GCCCAGAATCCAAACAGGCT

60.61

171

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGGAACTGGCCCTACTTCAG

59.75

GCCCAGAATCCAAACAGGCT

60.61

178

PCR template sequence:

GGGGGAACTGGCCCTACTTCAGACACAGGCTGGGGTTGCATGCTTCGGTGTGGACAGATGATCTTTGCCCAGGCCCTGGTATGCCGGCACTTAGGTCGAGCCACTTTGACATATGATACTCTCCGGTTTGCTGAATTTGAAGATTTCCCTGAGACCTCAGAGCCTGTTTGGATTCTGGGCAGAAAATACAGCATTTTCAC

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

1

Interacting miRNAs (#binding sites)

mmu-miR-467b-5p(1)

siRNAs for circular RNA silencing
Junction sequence

CACTTAGGTCGAGCCACTTTGACATA

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATG4B_273_ORF_1

0.4252

0.119186201

0.171522794

333

ORF sequence:

ATGCTTCGGTGTGGACAGATGATCTTTGCCCAGGCCCTGGTATGCCGGCACTTAGGTCGAGCCACTTTGACATATGATACTCTCCGGTTTGCTGAATTTGAAGATTTCCCTGAGACCTCAGAGCCTGTTTGGATTCTGGGCAGAAAATACAGCATTTTCACAGAGAAGGACGAAATCTTGTCTGATGTTGCATCCAGACTTTGGTTTACATACAGGAGAAACTTTCCAGCTATTGGGGGAACTGGCCCTACTTCAGACACAGGCTGGGGTTGCATGCTTCGGTGTGGACAGATGATCTTTGCCCAGGCCCTGGTATGCCGGCACTTAGGTCGA

Peptide sequence:

MLRCGQMIFAQALVCRHLGRATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILSDVASRLWFTYRRNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGR

IRESfinder result

IRESfinder score

0.607339849

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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