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mmu_circPitpnm3_361
Basic information of circular RNA
PanCircBase ID:
mmu_circPitpnm3_361
mm39_Chr. Position ID:
chr11|71965244|71983401|-
Gene name:
Pitpnm3
Transcript:
ENSMUST00000075258.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,540,18109
Genomic length:
18157
Exon/intron sizes in nt:
236,77,48
Flanking exon/introns:
chr11:71962414-71965244|chr11:71983401-72003082
Splice length:
361
Other database IDs:
circAtlas: mmu-Pitpnm3_0018
Human Ortholog IDs:
Mature spliced Sequence:
GAGACGGGGCCACAGCGTGCACATCCAGCATCCTGCAGGAGAAGCAGCGAGAACTGTACCGGGTGTCCCTCAGAAGGCAGAGGTTCCCAGCCCAAGGAAGTATCGAGATTCATGAAGATGGCGAGGAAGGCTGCTCACAGCGCTCCTGCAAGACACACGTCCTTCTGCTGGTGCTGCATGGGGGCAACGTCCTGGACACCGGCTCTGGTGACCCTTCCTGCAAGGCGGCCGACATTCACACTTTCAGCTCTGTGCTGGAGAAGGTCATGCGCGCCCACTTCCCTGCTGCCCTGGGACACATCCTCATCAAGTTTGTCCCTTGTCCTGCCATCTGCTCGGAGGCTTTCTCGCTCGTCTCTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGGGACACATCCTCATC
59.53
GACACCCGGTACAGTTCTCG
60.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCTGGGACACATCCTCATC
59.53
GGACACCCGGTACAGTTCTC
59.75
141
PCR template sequence:
AGGTCATGCGCGCCCACTTCCCTGCTGCCCTGGGACACATCCTCATCAAGTTTGTCCCTTGTCCTGCCATCTGCTCGGAGGCTTTCTCGCTCGTCTCTAAGAGACGGGGCCACAGCGTGCACATCCAGCATCCTGCAGGAGAAGCAGCGAGAACTGTACCGGGTGTCCCTCAGAAGGCAGAGGTTCCCAGCCCAAGGAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-431-5p(1), mmu-miR-1198-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CGCTCGTCTCTAAGAGACGGGGCCAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPITPNM3_361_ORF_1
0.8272
0.20931756
0.821836189
609
ORF sequence:
ATGAAGATGGCGAGGAAGGCTGCTCACAGCGCTCCTGCAAGACACACGTCCTTCTGCTGGTGCTGCATGGGGGCAACGTCCTGGACACCGGCTCTGGTGACCCTTCCTGCAAGGCGGCCGACATTCACACTTTCAGCTCTGTGCTGGAGAAGGTCATGCGCGCCCACTTCCCTGCTGCCCTGGGACACATCCTCATCAAGTTTGTCCCTTGTCCTGCCATCTGCTCGGAGGCTTTCTCGCTCGTCTCTAAGAGACGGGGCCACAGCGTGCACATCCAGCATCCTGCAGGAGAAGCAGCGAGAACTGTACCGGGTGTCCCTCAGAAGGCAGAGGTTCCCAGCCCAAGGAAGTATCGAGATTCATGAAGATGGCGAGGAAGGCTGCTCACAGCGCTCCTGCAAGACACACGTCCTTCTGCTGGTGCTGCATGGGGGCAACGTCCTGGACACCGGCTCTGGTGACCCTTCCTGCAAGGCGGCCGACATTCACACTTTCAGCTCTGTGCTGGAGAAGGTCATGCGCGCCCACTTCCCTGCTGCCCTGGGACACATCCTCATCAAGTTTGTCCCTTGTCCTGCCATCTGCTCGGAGGCTTTCTCGCTCGTCTCT
Peptide sequence:
MKMARKAAHSAPARHTSFCWCCMGATSWTPALVTLPARRPTFTLSALCWRRSCAPTSLLPWDTSSSSLSLVLPSARRLSRSSLRDGATACTSSILQEKQRELYRVSLRRQRFPAQGSIEIHEDGEEGCSQRSCKTHVLLLVLHGGNVLDTGSGDPSCKAADIHTFSSVLEKVMRAHFPAALGHILIKFVPCPAICSEAFSLVS
IRESfinder result
IRESfinder score
0.40801867
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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