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mmu_circPsmd1_220
Basic information of circular RNA
PanCircBase ID:
mmu_circPsmd1_220
mm39_Chr. Position ID:
chr1|86046231|86054280|+
Gene name:
Psmd1
Transcript:
ENSMUST00000139715.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
17,18
Exon/intron offsets:
0,7946
Genomic length:
8049
Exon/intron sizes in nt:
1,17,103
Flanking exon/introns:
chr1:86044411-86046231|chr1:86054280-86055857
Splice length:
220
Other database IDs:
CIRCpedia: MMU_CIRCpedia_213412
circBase: hsa_circ_0058640, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_39987
Human Ortholog IDs:
Mature spliced Sequence:
GAAGCAATTAATTTACTAGAGCCAATGACCAACGACCCTGTGAACTACGTGAGGCAAGGGGCTCTGATAGCTTCAGCTCTCATCATGATCCAACAGACTGAGATCACGTGTCCAAAGGTGAATCAGTTCCGGCAGCTGTATTCCAAAGTCATCAATGACAAACATGATGATGTCATGGCCAAATTTGGCGCTATTCTGGCCCAAGGCATACTGGATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCCGGCAGCTGTATTCC
60.11
AGTTCACAGGGTCGTTGGTC
59.89
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCCGGCAGCTGTATTCC
60.11
GTTCACAGGGTCGTTGGTCA
60.18
141
PCR template sequence:
AATCAGTTCCGGCAGCTGTATTCCAAAGTCATCAATGACAAACATGATGATGTCATGGCCAAATTTGGCGCTATTCTGGCCCAAGGCATACTGGATGCAGGAAGCAATTAATTTACTAGAGCCAATGACCAACGACCCTGTGAACTACGTGAGGCAAGGGGCTCTGATAGCTTCAGCTCTCATCATGATCCAACAGACTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-433-3p(1), mmu-miR-22-3p(1), mmu-miR-127-5p(1), mmu-miR-532-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATACTGGATGCAGGAAGCAATTAATT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSMD1_220_ORF_1
1.125
0.314894393
0.545577098
285
ORF sequence:
ATGACAAACATGATGATGTCATGGCCAAATTTGGCGCTATTCTGGCCCAAGGCATACTGGATGCAGGAAGCAATTAATTTACTAGAGCCAATGACCAACGACCCTGTGAACTACGTGAGGCAAGGGGCTCTGATAGCTTCAGCTCTCATCATGATCCAACAGACTGAGATCACGTGTCCAAAGGTGAATCAGTTCCGGCAGCTGTATTCCAAAGTCATCAATGACAAACATGATGATGTCATGGCCAAATTTGGCGCTATTCTGGCCCAAGGCATACTGGATGCA
Peptide sequence:
MTNMMMSWPNLALFWPKAYWMQEAINLLEPMTNDPVNYVRQGALIASALIMIQQTEITCPKVNQFRQLYSKVINDKHDDVMAKFGAILAQGILDA
IRESfinder result
IRESfinder score
0.179046871
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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