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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
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