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mmu_circPsme4_613
Basic information of circular RNA
PanCircBase ID:
mmu_circPsme4_613
mm39_Chr. Position ID:
chr11|30787281|30793588|+
Gene name:
Psme4
Transcript:
ENSMUST00000041231.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
28,29,30,31,32
Exon/intron offsets:
0,1603,4287,4709,6225
Genomic length:
6307
Exon/intron sizes in nt:
210,137,54,130,82
Flanking exon/introns:
chr11:30785467-30787281|chr11:30793588-30795179
Splice length:
613
Other database IDs:
circAtlas: mmu-Psme4_0069
Human Ortholog IDs:
Mature spliced Sequence:
GGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTTCAGGGCTTAGCCAAGCAATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTGCTGGTATTCTCAAGC
60.16
CTGGCCAGGTCTGCACAATA
60.04
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTGCTGGTATTCTCAAGC
60.16
GGCCAGGTCTGCACAATACA
60.32
156
PCR template sequence:
GCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATCAGGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-181b-5p(1), mmu-miR-3065-5p(1), mmu-miR-3470b(1), mmu-miR-296-3p(1), mmu-miR-181d-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCTTATGAAATCAGGCGCCTTATATT
siRNA sets
ATATAAGGCGCCTGATTTC, TATAAGGCGCCTGATTTCA, ATAAGGCGCCTGATTTCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPSME4_613_ORF_1
0.9749
-0.020212759
0.719080168
621
ORF sequence:
ATGAAATCAGGCGCCTTATATTGTCTACTTGGAAATCACAGTGGTGTGTGCCTGGCAAACCTTCATGATTGGGACTGTATTGTGCAGACCTGGCCAGCACTTGTTTCTTCAGGGCTTAGCCAAGCAATGTCACTGGAAAAGCCATCAATAGTGAGACTATTTGATGACCTTGCTGAAAAGATTCATAGACAATATGAAACAATTGGCTTGGATTTTACAATTCCAAAGTCATGTGCTGCAATAGCAGAATTACTTCAACAATCAAAGAATCCTTCCATTAGCCAGACACTACTTAGCCCAGAAAAGATTAAAGAAGGACAGAAGCGTCAACAAGATAAGAATGCTGATGCCCTAAGGAACTATGAATGTTTGGTAAATACTTTACTAGATGGTGTGGAGCAAAGAAATCTGCCTTGGAAATTTGAGCATATAGGAATCGGGCTTCTGTCTCTACTCCTAAGGGATGACAGAGTGTTGCCTCTTCGTGCCATACGTTTTTTTGTTGAAAATCTCAACCATGATGCAATTGTTGTTCGAAAGATGGCTATCTCAGCTGTTGCTGGTATTCTCAAGCAGCTAAAGAGAACTCACAAAAAGCTGACTATCAACCCTTATGAAATC
Peptide sequence:
MKSGALYCLLGNHSGVCLANLHDWDCIVQTWPALVSSGLSQAMSLEKPSIVRLFDDLAEKIHRQYETIGLDFTIPKSCAAIAELLQQSKNPSISQTLLSPEKIKEGQKRQQDKNADALRNYECLVNTLLDGVEQRNLPWKFEHIGIGLLSLLLRDDRVLPLRAIRFFVENLNHDAIVVRKMAISAVAGILKQLKRTHKKLTINPYEI
IRESfinder result
IRESfinder score
0.575311601
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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