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mmu_circPicalm_356

Basic information of circular RNA
PanCircBase ID:

mmu_circPicalm_356

mm39_Chr. Position ID:

chr7|89838357|89840961|+

Gene name:

Picalm

Transcript:

ENSMUST00000207225.2

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

13,14,15,16

Exon/intron offsets:

0,2006,2209,2504

Genomic length:

2604

Exon/intron sizes in nt:

10,81,17,31,100

Flanking exon/introns:

chr7:89826811-89838357|chr7:89840961-89844862

Splice length:

356

Other database IDs:

circAtlas: mmu-Picalm_0017

circBase: hsa_circ_0003695, circAtlas: hsa-PICALM_0016, CIRCpedia: HSA_CIRCpedia_5869

Human Ortholog IDs:
Mature spliced Sequence:

GATTCAGTCCTTCTCCAGTTGCACAGCCACATTCTTCAGCTGGCCTTAATGTTGACTTTGAATCTGTGTTTGGAAATAAATCTACGAATGTTGCTGTAGATTCTGGTGGTGGACTTCTCAAACCAACAGTGGCCTCCCAGAACCAGAGTCTTCCTGTTGCCAAACTTCCGCCTAACAAATTAGTGTCTGACGACTTGGATTCATCTTTAGCCAACCTTGTGGGCAATCTTGGCATTGGAAATGGAACCACTAAGAATGATGTAAGTTGGAGTCAACCAGGTGAAAAGAAGTTAACTGGAGGATCTAACTGGCAACCAAAGGTTGCACCAACAACTGCCTGGAGCGCTGCAACAATG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GTTGGAGTCAACCAGGTGAA

57.66

AGTCAACATTAAGGCCAGCTGA

59.96

149

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGGAGTCAACCAGGTGAAAAGA

59.49

AGTCAACATTAAGGCCAGCTGA

59.96

147

PCR template sequence:

TGATGTAAGTTGGAGTCAACCAGGTGAAAAGAAGTTAACTGGAGGATCTAACTGGCAACCAAAGGTTGCACCAACAACTGCCTGGAGCGCTGCAACAATGGATTCAGTCCTTCTCCAGTTGCACAGCCACATTCTTCAGCTGGCCTTAATGTTGACTTTGAATCTGTGTTTGGAAATAAATCTACGAATGTTGCTGTAGA

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

7

Interacting miRNAs (#binding sites)

mmu-miR-9-5p(1), mmu-miR-140-5p(1), mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-182-5p(1), mmu-miR-574-5p(1), mmu-miR-376a-3p(1)

siRNAs for circular RNA silencing
Junction sequence

CGCTGCAACAATGGATTCAGTCCTTC

siRNA sets

GAAGGACTGAATCCATTGT, ACTGAATCCATTGTTGCAG, TGAATCCATTGTTGCAGCG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCPICALM_356_ORF_1

1.0389

-0.153940524

0.038379847

102

ORF sequence:

ATGGATTCAGTCCTTCTCCAGTTGCACAGCCACATTCTTCAGCTGGCCTTAATGTTGACTTTGAATCTGTGTTTGGAAATAAATCTACGAATGTTGCTGTAG

Peptide sequence:

MDSVLLQLHSHILQLALMLTLNLCLEINLRMLL

IRESfinder result

IRESfinder score

0.682074969

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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