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mmu_circPsmd2_1005
Basic information of circular RNA
PanCircBase ID:
mmu_circPsmd2_1005
mm39_Chr. Position ID:
chr16|20478155|20481490|+
Gene name:
Psmd2
Transcript:
ENSMUST00000007212.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
13,14,15,16,17,18,19,20
Exon/intron offsets:
0,273,551,937,2159,2410,2687,3216
Genomic length:
3335
Exon/intron sizes in nt:
1,63,10,21,46,84,16,99,00,00,000
Flanking exon/introns:
chr16:20476811-20478155|chr16:20481490-20481812
Splice length:
1005
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGCAGGTGTGACGGCTCTAGCTTGTGGGATGATAGCAGTGGGGTCCTGCAATGGAGATGTCACTTCCACCATCCTTCAGACCATCATGGAGAAATCTGAGACTGAGCTCAAGGATACCTATGCTCGTTGGCTTCCTCTTGGCCTGGGCCTCAATCACTTGGGGAAAGGCGAAGCTATTGAGGCCATCCTGGCTGCCTTGGAGGTGGTGTCAGAGCCATTCCGCAGTTTTGCCAATACCCTGGTGGATGTATGTGCCTATGCAGGCTCTGGGAATGTGCTGAAGGTTCAGCAGCTCCTCCACATCTGTAGTGAGCACTTTGACTCTAAGGAAAAGGAGGAAGACAAAGACAAGAAGGAAAAGAAGGACAAGGACAAGAAGGAAGCCCCTGCTGACATGGGAGCACATCAGGGAGTAGCTGTTCTGGGCATTGCACTTATTGCTATGGGGGAAGAGATTGGTGCAGAGATGGCATTGCGAACTTTTGGTCACTTGCTGAGATATGGGGAGCCTACCCTCCGTCGCGCTGTACCTTTAGCACTGGCACTAATTTCTGTTTCAAATCCACGACTCAACATCCTGGATACGCTAAGCAAATTCTCTCATGATGCTGATCCAGAAGTTTCCTATAACTCCATCTTTGCTATGGGCATGGTGGGCAGTGGTACCAATAATGCCCGTCTGGCTGCAATGTTGCGCCAGTTAGCTCAATATCATGCCAAGGACCCCAATAACCTCTTCATGGTGCGCTTGGCACAGGGCTTGACACATTTAGGGAAGGGCACACTTACCCTCTGCCCCTATCACAGTGATCGGCAGCTCATGAGTCAAGTAGCGGTGGCAGGGCTACTCACGGTGCTTGTTTCTTTCCTGGATGTTCGAAACATCATCCTAGGCAAGTCTCACTATGTCCTGTATGGGCTGGTAGCCGCCATGCAGCCTCGGATGCTGGTTACATTTGATGAGGAGCTGCGACCATTGCCAGTTTCTGTCCGTGTGGGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCTGTATGGGCTGGTAGC
59.89
CCCCACTGCTATCATCCCAC
59.89
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCTGTATGGGCTGGTAGC
59.89
ACATCTCCATTGCAGGACCC
59.74
158
PCR template sequence:
CTATGTCCTGTATGGGCTGGTAGCCGCCATGCAGCCTCGGATGCTGGTTACATTTGATGAGGAGCTGCGACCATTGCCAGTTTCTGTCCGTGTGGGTCAGGTGGCAGGTGTGACGGCTCTAGCTTGTGGGATGATAGCAGTGGGGTCCTGCAATGGAGATGTCACTTCCACCATCCTTCAGACCATCATGGAGAAATCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
18
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-130a-3p(1), mmu-miR-298-5p(1), mmu-miR-184-3p(1), mmu-miR-24-3p(1), mmu-miR-153-3p(1), mmu-miR-182-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-362-5p(1), mmu-miR-324-3p(1), mmu-miR-188-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCGTGTGGGTCAGGTGGCAGGTGTGA
siRNA sets
CACACCTGCCACCTGACCC, TCACACCTGCCACCTGACC, ACACCTGCCACCTGACCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSMD2_1005_ORF_1
1.18
0.32026135
0.999996281
1980
ORF sequence:
ATGATAGCAGTGGGGTCCTGCAATGGAGATGTCACTTCCACCATCCTTCAGACCATCATGGAGAAATCTGAGACTGAGCTCAAGGATACCTATGCTCGTTGGCTTCCTCTTGGCCTGGGCCTCAATCACTTGGGGAAAGGCGAAGCTATTGAGGCCATCCTGGCTGCCTTGGAGGTGGTGTCAGAGCCATTCCGCAGTTTTGCCAATACCCTGGTGGATGTATGTGCCTATGCAGGCTCTGGGAATGTGCTGAAGGTTCAGCAGCTCCTCCACATCTGTAGTGAGCACTTTGACTCTAAGGAAAAGGAGGAAGACAAAGACAAGAAGGAAAAGAAGGACAAGGACAAGAAGGAAGCCCCTGCTGACATGGGAGCACATCAGGGAGTAGCTGTTCTGGGCATTGCACTTATTGCTATGGGGGAAGAGATTGGTGCAGAGATGGCATTGCGAACTTTTGGTCACTTGCTGAGATATGGGGAGCCTACCCTCCGTCGCGCTGTACCTTTAGCACTGGCACTAATTTCTGTTTCAAATCCACGACTCAACATCCTGGATACGCTAAGCAAATTCTCTCATGATGCTGATCCAGAAGTTTCCTATAACTCCATCTTTGCTATGGGCATGGTGGGCAGTGGTACCAATAATGCCCGTCTGGCTGCAATGTTGCGCCAGTTAGCTCAATATCATGCCAAGGACCCCAATAACCTCTTCATGGTGCGCTTGGCACAGGGCTTGACACATTTAGGGAAGGGCACACTTACCCTCTGCCCCTATCACAGTGATCGGCAGCTCATGAGTCAAGTAGCGGTGGCAGGGCTACTCACGGTGCTTGTTTCTTTCCTGGATGTTCGAAACATCATCCTAGGCAAGTCTCACTATGTCCTGTATGGGCTGGTAGCCGCCATGCAGCCTCGGATGCTGGTTACATTTGATGAGGAGCTGCGACCATTGCCAGTTTCTGTCCGTGTGGGTCAGGTGGCAGGTGTGACGGCTCTAGCTTGTGGGATGATAGCAGTGGGGTCCTGCAATGGAGATGTCACTTCCACCATCCTTCAGACCATCATGGAGAAATCTGAGACTGAGCTCAAGGATACCTATGCTCGTTGGCTTCCTCTTGGCCTGGGCCTCAATCACTTGGGGAAAGGCGAAGCTATTGAGGCCATCCTGGCTGCCTTGGAGGTGGTGTCAGAGCCATTCCGCAGTTTTGCCAATACCCTGGTGGATGTATGTGCCTATGCAGGCTCTGGGAATGTGCTGAAGGTTCAGCAGCTCCTCCACATCTGTAGTGAGCACTTTGACTCTAAGGAAAAGGAGGAAGACAAAGACAAGAAGGAAAAGAAGGACAAGGACAAGAAGGAAGCCCCTGCTGACATGGGAGCACATCAGGGAGTAGCTGTTCTGGGCATTGCACTTATTGCTATGGGGGAAGAGATTGGTGCAGAGATGGCATTGCGAACTTTTGGTCACTTGCTGAGATATGGGGAGCCTACCCTCCGTCGCGCTGTACCTTTAGCACTGGCACTAATTTCTGTTTCAAATCCACGACTCAACATCCTGGATACGCTAAGCAAATTCTCTCATGATGCTGATCCAGAAGTTTCCTATAACTCCATCTTTGCTATGGGCATGGTGGGCAGTGGTACCAATAATGCCCGTCTGGCTGCAATGTTGCGCCAGTTAGCTCAATATCATGCCAAGGACCCCAATAACCTCTTCATGGTGCGCTTGGCACAGGGCTTGACACATTTAGGGAAGGGCACACTTACCCTCTGCCCCTATCACAGTGATCGGCAGCTCATGAGTCAAGTAGCGGTGGCAGGGCTACTCACGGTGCTTGTTTCTTTCCTGGATGTTCGAAACATCATCCTAGGCAAGTCTCACTATGTCCTGTATGGGCTGGTAGCCGCCATGCAGCCTCGGATGCTGGTTACATTTGATGAGGAGCTGCGACCATTGCCAGTTTCTGTCCGTGTGGGTCAG
Peptide sequence:
MIAVGSCNGDVTSTILQTIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEPFRSFANTLVDVCAYAGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALIAMGEEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPEVSYNSIFAMGMVGSGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCPYHSDRQLMSQVAVAGLLTVLVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPLPVSVRVGQVAGVTALACGMIAVGSCNGDVTSTILQTIMEKSETELKDTYARWLPLGLGLNHLGKGEAIEAILAALEVVSEPFRSFANTLVDVCAYAGSGNVLKVQQLLHICSEHFDSKEKEEDKDKKEKKDKDKKEAPADMGAHQGVAVLGIALIAMGEEIGAEMALRTFGHLLRYGEPTLRRAVPLALALISVSNPRLNILDTLSKFSHDADPEVSYNSIFAMGMVGSGTNNARLAAMLRQLAQYHAKDPNNLFMVRLAQGLTHLGKGTLTLCPYHSDRQLMSQVAVAGLLTVLVSFLDVRNIILGKSHYVLYGLVAAMQPRMLVTFDEELRPLPVSVRVGQ
IRESfinder result
IRESfinder score
0.484733034
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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