top of page

mmu_circR3hdm2_456

Basic information of circular RNA
PanCircBase ID:

mmu_circR3hdm2_456

mm39_Chr. Position ID:

chr10|127280144|127290625|+

Gene name:

R3hdm2

Transcript:

ENSMUST00000166820.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

4,5,6,7

Exon/intron offsets:

0,7716,8416,10354

Genomic length:

10481

Exon/intron sizes in nt:

2,00,42,87,127

Flanking exon/introns:

chr10:127236062-127280144|chr10:127290625-127293518

Splice length:

456

Other database IDs:

CIRCpedia: MMU_CIRCpedia_6929, circAtlas: mmu-R3hdm2_0004

circAtlas: hsa-R3HDM2_0004, CIRCpedia: HSA_CIRCpedia_66597

Human Ortholog IDs:
Mature spliced Sequence:

AAATCCATAAAAGCTGCTGTACCCTGCTGCAGAACATGTCTAACAGTAACACTACTCAGGAGACTCTGGAAATAATGAAAGAATCAGAAAAAAAACTGGTGGAAGAATCTGTAAACAAAAATAAATTTATATCCAAAACTCCAAGTAAGGAAGACGTCGAGAAGGAGGGTGAAGAGAATGGTCTGCGTCAGGAGACACAGAGACGGACATCCAGTCATGGCCATGCCAGGAAAAGAGCCAAGTCTAATTCCAAACTCAAGTTGGTGCGCAGTCTGGCAGTCTGTGAGGAATCCTCCACTCCATTTGTCGATGGGCCACTAGACACCCAGGATATAATTCAACTGCACATCAGCTGCCCCTCTGACAAGGAGGAAGAAAAGTCCACAAAAGATGTCTCTGAAAAGGAAGACAAGGACAAAAGCAAAGAAAAGGTCCCAAGGAAGATGCTATCCAGAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACAAGGAGGAAGAAAAGTCCACA

59.8

TCCAGAGTCTCCTGAGTAGTGT

59.35

163

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CTCTGACAAGGAGGAAGAAAAGT

58.03

TAGACATGTTCTGCAGCAGGG

60.07

140

PCR template sequence:

CCCTCTGACAAGGAGGAAGAAAAGTCCACAAAAGATGTCTCTGAAAAGGAAGACAAGGACAAAAGCAAAGAAAAGGTCCCAAGGAAGATGCTATCCAGAGAAATCCATAAAAGCTGCTGTACCCTGCTGCAGAACATGTCTAACAGTAACACTACTCAGGAGACTCTGGAAATAATGAAAGAATCAGAAAAAAAACTGGT

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-214-3p(1), mmu-miR-335-3p(1)

siRNAs for circular RNA silencing
Junction sequence

ATGCTATCCAGAGAAATCCATAAAAG

siRNA sets

CTTTTATGGATTTCTCTGG, TTTTATGGATTTCTCTGGA, TATGGATTTCTCTGGATAG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCR3HDM2_456_ORF_1

1.065

0.253801927

0.983296264

876

ORF sequence:

ATGTCTAACAGTAACACTACTCAGGAGACTCTGGAAATAATGAAAGAATCAGAAAAAAAACTGGTGGAAGAATCTGTAAACAAAAATAAATTTATATCCAAAACTCCAAGTAAGGAAGACGTCGAGAAGGAGGGTGAAGAGAATGGTCTGCGTCAGGAGACACAGAGACGGACATCCAGTCATGGCCATGCCAGGAAAAGAGCCAAGTCTAATTCCAAACTCAAGTTGGTGCGCAGTCTGGCAGTCTGTGAGGAATCCTCCACTCCATTTGTCGATGGGCCACTAGACACCCAGGATATAATTCAACTGCACATCAGCTGCCCCTCTGACAAGGAGGAAGAAAAGTCCACAAAAGATGTCTCTGAAAAGGAAGACAAGGACAAAAGCAAAGAAAAGGTCCCAAGGAAGATGCTATCCAGAGAAATCCATAAAAGCTGCTGTACCCTGCTGCAGAACATGTCTAACAGTAACACTACTCAGGAGACTCTGGAAATAATGAAAGAATCAGAAAAAAAACTGGTGGAAGAATCTGTAAACAAAAATAAATTTATATCCAAAACTCCAAGTAAGGAAGACGTCGAGAAGGAGGGTGAAGAGAATGGTCTGCGTCAGGAGACACAGAGACGGACATCCAGTCATGGCCATGCCAGGAAAAGAGCCAAGTCTAATTCCAAACTCAAGTTGGTGCGCAGTCTGGCAGTCTGTGAGGAATCCTCCACTCCATTTGTCGATGGGCCACTAGACACCCAGGATATAATTCAACTGCACATCAGCTGCCCCTCTGACAAGGAGGAAGAAAAGTCCACAAAAGATGTCTCTGAAAAGGAAGACAAGGACAAAAGCAAAGAAAAGGTCCCAAGGAAGATGCTATCCAGA

Peptide sequence:

MSNSNTTQETLEIMKESEKKLVEESVNKNKFISKTPSKEDVEKEGEENGLRQETQRRTSSHGHARKRAKSNSKLKLVRSLAVCEESSTPFVDGPLDTQDIIQLHISCPSDKEEEKSTKDVSEKEDKDKSKEKVPRKMLSREIHKSCCTLLQNMSNSNTTQETLEIMKESEKKLVEESVNKNKFISKTPSKEDVEKEGEENGLRQETQRRTSSHGHARKRAKSNSKLKLVRSLAVCEESSTPFVDGPLDTQDIIQLHISCPSDKEEEKSTKDVSEKEDKDKSKEKVPRKMLSR

IRESfinder result

IRESfinder score

0.292997256

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

logo.png

Institute of Life sciences, Bhubaneswar, India

bottom of page