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mmu_circNploc4_420

Basic information of circular RNA
PanCircBase ID:

mmu_circNploc4_420

mm39_Chr. Position ID:

chr11|120309894|120323954|-

Gene name:

Nploc4

Transcript:

ENSMUST00000044271.15

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

5,4,3,2

Exon/intron offsets:

0,2296,9455,13979

Genomic length:

14060

Exon/intron sizes in nt:

49,177,113,81

Flanking exon/introns:

chr11:120309165-120309894|chr11:120323954-120328324

Splice length:

420

Other database IDs:

circAtlas: mmu-Nploc4_0033

circBase: hsa_circ_0046206, circAtlas: hsa-NPLOC4_0092, CIRCpedia: HSA_CIRCpedia_22779

Human Ortholog IDs:
Mature spliced Sequence:

ATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCTTCCAAAACAACGGCTTCTCAGTTTACATCAATAGAAACAAGACTGGAGAGATAACAGCATCGTCCAGCAAATCCCTCCATTTGCTAAAAATCAAGCATGGCGATTTGTTGTTCCTGTTTCCCTCAAGCCTTGCTGGACCCTCGTCTGAAATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAGCAAGCAGGATGGGAAGA

60.03

GCCGTCTCTCTCTTCGTAGC

59.97

156

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCAGCAAGCAGGATGGGAAG

60.03

GCCGTCTCTCTCTTCGTAGC

59.97

157

PCR template sequence:

ATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAGATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCT

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-541-5p(1), mmu-miR-3065-5p(1), mmu-miR-7a-1-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TGTCCCACTGGAGATAATCCGTGTCC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCNPLOC4_420_ORF_1

0.9571

0.274228593

0.870248243

591

ORF sequence:

ATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAGATAATCCGTGTCCAGTCCCCTGATGGCGTGAAGAGGATCACAGCTACGAAGAGAGAGACGGCTGCCACCTTCCTGAAAAAGGTTGCAAAGGAGTTTGGCTTCCAAAACAACGGCTTCTCAGTTTACATCAATAGAAACAAGACTGGAGAGATAACAGCATCGTCCAGCAAATCCCTCCATTTGCTAAAAATCAAGCATGGCGATTTGTTGTTCCTGTTTCCCTCAAGCCTTGCTGGACCCTCGTCTGAAATGGAAACATCGACCTCGGTAGGGTTAAAGGCCTTTGGTGCTCCTAACGTGGTTGAAGATGAGATCGATCAATACCTCAGCAAGCAGGATGGGAAGATTTACCGGAGCCGAGACCCACAGCTATGCCGCCATGGTCCCTTGGGCAAGTGTGTGCATTGTGTCCCACTGGAG

Peptide sequence:

METSTSVGLKAFGAPNVVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLEIIRVQSPDGVKRITATKRETAATFLKKVAKEFGFQNNGFSVYINRNKTGEITASSSKSLHLLKIKHGDLLFLFPSSLAGPSSEMETSTSVGLKAFGAPNVVEDEIDQYLSKQDGKIYRSRDPQLCRHGPLGKCVHCVPLE

IRESfinder result

IRESfinder score

0.399731545

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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