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mmu_ciPsmd2_1138
Basic information of circular RNA
PanCircBase ID:
mmu_ciPsmd2_1138
mm39_Chr. Position ID:
chr16|20479176|20480314|+
Gene name:
Psmd2
Transcript:
ENSMUST00000007212.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
16
Exon/intron offsets:
0
Genomic length:
1138
Exon/intron sizes in nt:
1138
Flanking exon/introns:
chr16:20479176-20480314
Splice length:
1138
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGTAGCCCAGAGTAGACTGGAATATGGGGGTAGTAGGTGCTGGGGGTTAAACCTAGGGCCTTATGCATACATGGAAGTGATTCACCACCACACTACACTTTAGTCCTGCCTAATTCTGGTTTTGGTGGCTATTATTTGCCATACGTGCTTGTGTGTAAATGCATAGAGGTGTCAGTCTTCACCTTCTGCCTTCTCTGAAACAGGGTCTCTGTCTTAATCAACACTCTTGCTGTGAAGAAACACCATGACCAAAGCAACACTTTTTTATTTATTTTATGTATGAGTACACTCACTGAAGACAGTGACAGTGTCTGGTGAGAAGAGGGCATTTGATCCCATTATAGATAGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGAAGAAGAGTCTGTGCTCTTAACCATGGAGCCATCTCTCTCTCCATAAGGCAGCTCTTATGAAGGAGAACATGTAATTGGGGCTGGCTTACAGTTCAGAGGTTTAGTCCGTTGTCATGGGAGAAAGTATGATGACATGCAGACAGACATGGTGCTAGAGCAGTGGTTCTCAACCTTCCTACTGCTCTCACCCTTTCATACAGTTTCTCATGCTGTGGTGACTTCTAACTATAAAATGATTTTCATTGCTACTTCATAACTATAATTTTGCTACTGTTCTGAATTATAATATAAATGTCTAATGTTTTCTGATGGCCTTAGGGGACTCCTATGAAAGGGTTTTTCAACTCCCAGAAAGGGTTGAGACCCAAAGGTTGAGAACCACTATGCTAGCCAACTGACAGTTCTGTGTCCAGACCTGCGGGAAGCAGTCAGGCAGTAGGCCTAGGTTTGGCTTCTGATACTCCAAAGCCCATCCCTAGTGACACACTTCCTTCAACAAGGCCATACCTCAACATCCTTTTCAAATAATGCCATTCCCTAATAACCAAGCTTTATGGGGGCTATTTCTGTTCAAACCACCATAGTCTCTTATATTTCTCCTGATTAGCTGGTCCGAGAGCTTCCAGAGCACTAGGACTGCAGATGACCTCATGTTTGCACAGCGGACAGTTTTACCCAGTGAACTATCTCTGCCCAAACTTGTTTCTACCTCTTTTCCCAAACTATTTTATTTATTTTTATCACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTTTGCACAGCGGACAGTTT
59.9
CCCTAGGTTTAACCCCCAGC
59.74
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTTTGCACAGCGGACAGTTT
59.9
GCCCTAGGTTTAACCCCCAG
59.74
157
PCR template sequence:
CTCATGTTTGCACAGCGGACAGTTTTACCCAGTGAACTATCTCTGCCCAAACTTGTTTCTACCTCTTTTCCCAAACTATTTTATTTATTTTTATCACCAGGTGAGTAGCCCAGAGTAGACTGGAATATGGGGGTAGTAGGTGCTGGGGGTTAAACCTAGGGCCTTATGCATACATGGAAGTGATTCACCACCACACTACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-140-5p(1), mmu-let-7e-5p(1), mmu-let-7b-5p(1), mmu-let-7c-5p(1), mmu-miR-326-3p(1), mmu-miR-185-5p(1), mmu-let-7d-5p(1), mmu-miR-22-3p(1), mmu-miR-98-5p(1), mmu-miR-466b-3p(1), mmu-miR-202-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTTATCACCAGGTGAGTAGCCCAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIPSMD2_1138_ORF_2
0.8531
-0.339137865
0.014646399
123
ORF sequence:
ATGACCTCATGTTTGCACAGCGGACAGTTTTACCCAGTGAACTATCTCTGCCCAAACTTGTTTCTACCTCTTTTCCCAAACTATTTTATTTATTTTTATCACCAGGTGAGTAGCCCAGAGTAG
Peptide sequence:
MTSCLHSGQFYPVNYLCPNLFLPLFPNYFIYFYHQVSSPE
IRESfinder result
IRESfinder score
0.814565031
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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