top of page

mmu_circPkhd1_370

Basic information of circular RNA
PanCircBase ID:

mmu_circPkhd1_370

mm39_Chr. Position ID:

chr1|20484444|20520601|-

Gene name:

Pkhd1

Transcript:

ENSMUST00000088448.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

37,36

Exon/intron offsets:

0,36000

Genomic length:

36157

Exon/intron sizes in nt:

2,13,157

Flanking exon/introns:

chr1:20462443-20484444|chr1:20520601-20573165

Splice length:

370

Other database IDs:

circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_146607

Human Ortholog IDs:
Mature spliced Sequence:

GGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGAAGTGTCCATTCCACTCCC

60.34

CGTGTGGCACTCTTTGAGGA

60.25

152

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGAAGTGTCCATTCCACTCCC

60.34

TCGTGTGGCACTCTTTGAGG

60.25

153

PCR template sequence:

AAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCATGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCG

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

2

Interacting miRNAs (#binding sites)

mmu-miR-138-5p(1), mmu-miR-673-5p(1)

siRNAs for circular RNA silencing
Junction sequence

CTTTCCCTGCATGGGCAACTTTTCCT

siRNA sets

GAAAAGTTGCCCATGCAGG, AGGAAAAGTTGCCCATGCA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCPKHD1_370_ORF_1

0.8398

0.151869589

0.434527296

390

ORF sequence:

ATGGAACTCTTTCCCTGCATGGGCAACTTTTCCTTCCAATTCTGCCGAAGGTGGTCCAGGCCTCACAGTTGGTTTCCTCAAAGAGTGCCACACGATGGCGACAGTGTCACAGTGGAGACCGGTCACCTGCTACTGCTTGATGCGAACACTAGCTTCCTGAACTCCCTGCACATTAAAGGTGGCAAGCTGATCTTCATGGATCCAGGACCCATTGAGCTCAGAGCCCACTCCATCCTTATTACAGATGGTGGAGAGCTCCATATTGGATCTGAGGAAAAGCCTTTCCAAGGCAAAGCTCGGATCAAAATCTATGGAAGTGTCCATTCCACTCCCTTCTTTCCCTATGGAGTCAAGTTCCTAGCTGTGAGGAATGGAACTCTTTCCCTGCAT

Peptide sequence:

MELFPCMGNFSFQFCRRWSRPHSWFPQRVPHDGDSVTVETGHLLLLDANTSFLNSLHIKGGKLIFMDPGPIELRAHSILITDGGELHIGSEEKPFQGKARIKIYGSVHSTPFFPYGVKFLAVRNGTLSLH

IRESfinder result

IRESfinder score

0.657419386

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

logo.png

Institute of Life sciences, Bhubaneswar, India

bottom of page