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mmu_circPtprm_386
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprm_386
mm39_Chr. Position ID:
chr17|67219347|67227291|-
Gene name:
Ptprm
Transcript:
ENSMUST00000037974.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
14,13,12
Exon/intron offsets:
0,6671,7670
Genomic length:
7944
Exon/intron sizes in nt:
75,37,274
Flanking exon/introns:
chr17:67198051-67219347|chr17:67227291-67247477
Splice length:
386
Other database IDs:
CIRCpedia: MMU_CIRCpedia_26674, circAtlas: mmu-Ptprm_0002
circBase: hsa_circ_0108934, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_121272
Human Ortholog IDs:
Mature spliced Sequence:
TGTCTATCAAATCGTTGTTGAGGAAGAACGTCCTCGGAGAACTAAGAAGACAACAGAGATCTTGAAGTGTTACCCGGTGCCAATTCACTTCCAGAATGCGTCCATCCTGAACTCACAGTACTACTTTGCTGCAGAATTTCCTGCAGACAGCCTCCAAGCTGCTCAACCATTTACCATTGGTGACAATAAGACATACAATGGCTACTGGAACACCCCCCTCCTCCCCCATAAAAGCTACAGAATTTATTACCAAGCTGCTAGTCGAGCCAATGGGGAAACCAAAATTGACTGTGTCCGAGTGGCCACAAAAGCTGCGATAATCGTGACTCAGCTTACAACACCTTACATTCGCATCGCCCCTGCTGCAGGCGACGGCCAACTAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCACAAAAGCTGCGATAA
59.47
TGAATTGGCACCGGGTAACA
59.89
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCCACAAAAGCTGCGATAA
59.47
ATTGGCACCGGGTAACACTT
59.89
170
PCR template sequence:
GACTGTGTCCGAGTGGCCACAAAAGCTGCGATAATCGTGACTCAGCTTACAACACCTTACATTCGCATCGCCCCTGCTGCAGGCGACGGCCAACTAACAGTGTCTATCAAATCGTTGTTGAGGAAGAACGTCCTCGGAGAACTAAGAAGACAACAGAGATCTTGAAGTGTTACCCGGTGCCAATTCACTTCCAGAATGCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-434-5p(1), mmu-miR-96-5p(1), mmu-miR-297a-5p(1), mmu-miR-29b-2-5p(1), mmu-miR-1199-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCCAACTAACAGTGTCTATCAAATC
siRNA sets
TAGACACTGTTAGTTGGCC, ATAGACACTGTTAGTTGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.547951489
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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