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mmu_circPtprm_305
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprm_305
mm39_Chr. Position ID:
chr17|67247477|67251324|-
Gene name:
Ptprm
Transcript:
ENSMUST00000037974.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
11,10
Exon/intron offsets:
0,3645
Genomic length:
3847
Exon/intron sizes in nt:
1,03,202
Flanking exon/introns:
chr17:67227291-67247477|chr17:67251324-67260062
Splice length:
305
Other database IDs:
circAtlas: mmu-Ptprm_0018
circBase: hsa_circ_0046808, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_24429
Human Ortholog IDs:
Mature spliced Sequence:
ATCACCTACAAAGCAGTCAGTTCCTTTGACCCGGAAATAGATTTATCCAACCAAAGTGGGCGAGTTTCAAAACTGGGAAATGAAACCCATTTTCTGTTCTTTGGCCTGTATCCTGGAACGACGTACTCCTTCACCATCAGAGCCAGCACAGCGAAGGGGTTCGGACCTCCGGCAACAAACCAGTTCACCACAAAAATATCAGCACCATCCATGCCAGCCTATGAATTTGAGACACCTTTGAATCAGACTGATAATACAGTGACTGTGATGCTGAAACCTGCACAAAGCAGAGGGGCTCCAGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CATCCATGCCAGCCTATGAA
57.72
TGAAACTCGCCCACTTTGGT
60.11
169
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATCCATGCCAGCCTATGAA
57.72
CCCAGTTTTGAAACTCGCCC
59.69
177
PCR template sequence:
CATCCATGCCAGCCTATGAATTTGAGACACCTTTGAATCAGACTGATAATACAGTGACTGTGATGCTGAAACCTGCACAAAGCAGAGGGGCTCCAGTCAGATCACCTACAAAGCAGTCAGTTCCTTTGACCCGGAAATAGATTTATCCAACCAAAGTGGGCGAGTTTCAAAACTGGGAAATGAAACCCATTTTCTGTTCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-29b-1-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGCTCCAGTCAGATCACCTACAAAG
siRNA sets
TTTGTAGGTGATCTGACTG, TTGTAGGTGATCTGACTGG, TGTAGGTGATCTGACTGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRM_305_ORF_3
0.964
0.011835419
0.080019482
135
ORF sequence:
ATGCCAGCCTATGAATTTGAGACACCTTTGAATCAGACTGATAATACAGTGACTGTGATGCTGAAACCTGCACAAAGCAGAGGGGCTCCAGTCAGATCACCTACAAAGCAGTCAGTTCCTTTGACCCGGAAATAG
Peptide sequence:
MPAYEFETPLNQTDNTVTVMLKPAQSRGAPVRSPTKQSVPLTRK
IRESfinder result
IRESfinder score
0.641175797
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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