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mmu_circPsmd9_414
Basic information of circular RNA
PanCircBase ID:
mmu_circPsmd9_414
mm39_Chr. Position ID:
chr5|123372656|123379996|+
Gene name:
Psmd9
Transcript:
ENSMUST00000133386.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,4948,7238
Genomic length:
7340
Exon/intron sizes in nt:
10,32,09,102
Flanking exon/introns:
chr5:123366507-123372656|chr5:123379996-123381366
Splice length:
414
Other database IDs:
circAtlas: mmu-Psmd9_0001
circBase: hsa_circ_0008670, circAtlas: hsa-PSMD9_0001, CIRCpedia: HSA_CIRCpedia_7236
Human Ortholog IDs:
Mature spliced Sequence:
CAAAAAGGAATTGGCATGAACGAACCGCTGGTGGACTGTGAGGGCTATCCCCGGGCGGATGTGGACTTGTACCAGGTCCGAACAGCAAGGCACAACATCATCTGTCTCCAGAATGATCACAAGGCACTGATGAAGCAAGTGGAGGAGGCCCTGCACCAGCTGCACGCTCGGGACAAAGAGAAGCAGGCTCGGGACATGGCTGAAGCCCGAGAAGAGGCCATGAACCGCAGGCTGGCCTCCAACAGCCCCGTCCTGCCCCAGGCCTTTGCCAGAGTGAACAGTATCAGCCCCGGTTCCCCAGCCAGTATTGCGGGCCTGCAAGTGGATGACGAAATTGTGGAGTTCGGCTCCGTGAACACCCAAAACTTCCAGTCAGTGCAGAACGTGGGCACTGTGGTGCAGCATAGCGAGGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCCGTGAACACCCAAAAC
59.97
GCTGTTCGGACCTGGTACAA
59.97
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCCGTGAACACCCAAAAC
59.97
TTGCTGTTCGGACCTGGTAC
59.97
156
PCR template sequence:
CCTGCAAGTGGATGACGAAATTGTGGAGTTCGGCTCCGTGAACACCCAAAACTTCCAGTCAGTGCAGAACGTGGGCACTGTGGTGCAGCATAGCGAGGGGCAAAAAGGAATTGGCATGAACGAACCGCTGGTGGACTGTGAGGGCTATCCCCGGGCGGATGTGGACTTGTACCAGGTCCGAACAGCAAGGCACAACATCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-139-5p(1), mmu-miR-128-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCATAGCGAGGGGCAAAAAGGAATTG
siRNA sets
ATTCCTTTTTGCCCCTCGC,AATTCCTTTTTGCCCCTCG,TTCCTTTTTGCCCCTCGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSMD9_414_ORF_1
1.2564
0.565239232
0.994789624
813
ORF sequence:
ATGAACGAACCGCTGGTGGACTGTGAGGGCTATCCCCGGGCGGATGTGGACTTGTACCAGGTCCGAACAGCAAGGCACAACATCATCTGTCTCCAGAATGATCACAAGGCACTGATGAAGCAAGTGGAGGAGGCCCTGCACCAGCTGCACGCTCGGGACAAAGAGAAGCAGGCTCGGGACATGGCTGAAGCCCGAGAAGAGGCCATGAACCGCAGGCTGGCCTCCAACAGCCCCGTCCTGCCCCAGGCCTTTGCCAGAGTGAACAGTATCAGCCCCGGTTCCCCAGCCAGTATTGCGGGCCTGCAAGTGGATGACGAAATTGTGGAGTTCGGCTCCGTGAACACCCAAAACTTCCAGTCAGTGCAGAACGTGGGCACTGTGGTGCAGCATAGCGAGGGGCAAAAAGGAATTGGCATGAACGAACCGCTGGTGGACTGTGAGGGCTATCCCCGGGCGGATGTGGACTTGTACCAGGTCCGAACAGCAAGGCACAACATCATCTGTCTCCAGAATGATCACAAGGCACTGATGAAGCAAGTGGAGGAGGCCCTGCACCAGCTGCACGCTCGGGACAAAGAGAAGCAGGCTCGGGACATGGCTGAAGCCCGAGAAGAGGCCATGAACCGCAGGCTGGCCTCCAACAGCCCCGTCCTGCCCCAGGCCTTTGCCAGAGTGAACAGTATCAGCCCCGGTTCCCCAGCCAGTATTGCGGGCCTGCAAGTGGATGACGAAATTGTGGAGTTCGGCTCCGTGAACACCCAAAACTTCCAGTCAGTGCAGAACGTGGGCACTGTGGTGCAGCATAGCGAGGGG
Peptide sequence:
MNEPLVDCEGYPRADVDLYQVRTARHNIICLQNDHKALMKQVEEALHQLHARDKEKQARDMAEAREEAMNRRLASNSPVLPQAFARVNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNVGTVVQHSEGQKGIGMNEPLVDCEGYPRADVDLYQVRTARHNIICLQNDHKALMKQVEEALHQLHARDKEKQARDMAEAREEAMNRRLASNSPVLPQAFARVNSISPGSPASIAGLQVDDEIVEFGSVNTQNFQSVQNVGTVVQHSEG
IRESfinder result
IRESfinder score
0.21052165
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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