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mmu_circPpp4r1_1742
Basic information of circular RNA
PanCircBase ID:
mmu_circPpp4r1_1742
mm39_Chr. Position ID:
chr17|66110205|66138087|+
Gene name:
Ppp4r1
Transcript:
ENSMUST00000160664.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
3,4,5,6,7,8,9,10,11,12,13
Exon/intron offsets:
0,649,7327,8032,10247,10477,11095,12712,21049,26164,27786
Genomic length:
27882
Exon/intron sizes in nt:
85,107,143,147,108,66,159,128,530,173,96
Flanking exon/introns:
chr17:66090663-66110205|chr17:66138087-66139948
Splice length:
1742
Other database IDs:
circAtlas: mmu-Ppp4r1_0029
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_115520
Human Ortholog IDs:
Mature spliced Sequence:
CCCTGGACTTCGTCTCACAAGATGAAATGTTGACACCCTTGGGGAGGCTGGACAAGTATGCTGCAAGTGAGAACGTATTTAACAGACAAATGGTGGCCCGGAGTTTGCTGGATACTCTGAGGGAAGTCTGCGATGATGAGAGAGACTGCATTGCTGTCTTGGAAAGAATTAGCCGATTAGCTGATGACTCCGAACCAACTGTGAGAGCGGAGCTGATGGAACAAGTGCCGCACATTGCACTGTTTTGTCAAGAGAACCGGCCTTCTATACCGTATGCTTTTTCCAAGTACTTACTACCAATTGTGGTCAGATACCTCGCAGACCAGAATAACCAGGTGAGGAAAACCAGTCAGGCAGCTTTGCTGGCTCTGCTGGAGCAGGAACTGATTGAGCGATTTGACGTGGAGACCAAGGTGTGCCCTGTCCTCATAGACCTGACTGCCCCAGACAGCAATGATGATGTGAAGACAGAAGCTGTGGCTATAATGTGCAAGATGGCCCCCATGGTTGGGAAGGACATTACGGAGCGCCTCATCCTCCCCAGGTTCTGCGAGATGTGCTGTGACTGTCGAATGTTTCATGTCCGGAAGGTCTGCGCTGCCAATTTTGGAGATATTTGCAGTGTAGTTGGCCAACAAGCAACAGAAGAAATGTTGCTGCCCAGGTTCTTCCAGCTGTGCTCTGATAACGTGTGGGGCGTCCGAAAGGCCTGTGCTGAGTGCTTCATGGCTGTCTCCTGTGCAACATGTCAAGAAATCCGACGGACAAAGTTATCAGCACTATTTATTAACTTGATCAGTGATCCTTCACGTTGGGTTCGCCAAGCAGCCTTTCAGTCTCTGGGGCCTTTCATATCCACGTTTGCTAATCCATCAAGCTCGGGCCAGTGCTTTAAAGATGAGAGCAAGAACTCAGAAGACTCCTCGGCAGAAGACAAAGACAGGATGAGAGACAATGATGTCGTAGAAGAAGAGCATCGCAGGCCAGAGGACGCTCCTTCAGACCTCAGTGCCCCTCACTCCAGCGCCAGGCTGGAGAGCCTCGAAGGCTGTGCTGCCAAGACACCTGGGCACTCTGCAGGTGACGTGCCTGCTCCAGTGGACAGCTCCTTACTCTGTACTTTGTCCTCAGAGTCTCCTCAGGAAGCAGCTAGCAATGATGAGAATGGTAGAAAGCCTGACACCAACAGCAAGTCTGCGTCCCGGCCAGACGCTGGCACCAGCTCCCCAGAGGCCACTCCCTTAGACCAGGACATGTTCAACTCCTTCCATTTCTGGAGGACTCCTCTACCTAAAATAGATCTTGATAAAGAGCTCCAGCAGGACCCCGAGGAGAGACTCAGCCCAGAGAGAACAGGAGATGTACCTGCAGCCCCTCTACCAGGCCCTCCCAATATCACCATGGCTACCCGGAAGGAACTAGAAGAAATGATAGAAAACCTTGAGCCACACATGGATGACCCGGATGTGAAAGCACAGGTGGACGTGCTGTCGGCTGCCCTGCGAGCTTCCAGCCTGGATGCTCACGAAGAGACTGGTGGTGTAGAGCAGCGGAGTGAGCTACAAGATGAAGTGTGTGTCAGTGAGCTTCCAGACTGTAACATAAGTCACGACACTTGTGTGCCTTTGATCAGCGCTGCTGAGGAGAATGCGGAGGCCACTCCTGATTATGTCCATGGAGGTGCAGACGTAAGCCCTGGTGATGGCTTCAGCCCGGATGAAGATAGGAGACCCAAAGTCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGGAGGTGCAGACGTAAGC
60.11
CGGGCCACCATTTGTCTGTT
61.18
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGTCCATGGAGGTGCAGAC
59.75
CTTGCAGCATACTTGTCCAGC
59.87
141
PCR template sequence:
GGAGAATGCGGAGGCCACTCCTGATTATGTCCATGGAGGTGCAGACGTAAGCCCTGGTGATGGCTTCAGCCCGGATGAAGATAGGAGACCCAAAGTCCAGCCCTGGACTTCGTCTCACAAGATGAAATGTTGACACCCTTGGGGAGGCTGGACAAGTATGCTGCAAGTGAGAACGTATTTAACAGACAAATGGTGGCCCG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-103-3p(1), mmu-miR-322-5p(1), mmu-miR-130a-3p(1), mmu-miR-19a-3p(1), mmu-miR-152-3p(1), mmu-miR-148a-3p(1), mmu-miR-138-5p(1), mmu-miR-139-5p(1), mmu-miR-351-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-370-3p(1), mmu-miR-107-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACCCAAAGTCCAGCCCTGGACTTCGT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPP4R1_1742_ORF_1
1.0563
0.278874284
0.99996961
1749
ORF sequence:
ATGTTGACACCCTTGGGGAGGCTGGACAAGTATGCTGCAAGTGAGAACGTATTTAACAGACAAATGGTGGCCCGGAGTTTGCTGGATACTCTGAGGGAAGTCTGCGATGATGAGAGAGACTGCATTGCTGTCTTGGAAAGAATTAGCCGATTAGCTGATGACTCCGAACCAACTGTGAGAGCGGAGCTGATGGAACAAGTGCCGCACATTGCACTGTTTTGTCAAGAGAACCGGCCTTCTATACCGTATGCTTTTTCCAAGTACTTACTACCAATTGTGGTCAGATACCTCGCAGACCAGAATAACCAGGTGAGGAAAACCAGTCAGGCAGCTTTGCTGGCTCTGCTGGAGCAGGAACTGATTGAGCGATTTGACGTGGAGACCAAGGTGTGCCCTGTCCTCATAGACCTGACTGCCCCAGACAGCAATGATGATGTGAAGACAGAAGCTGTGGCTATAATGTGCAAGATGGCCCCCATGGTTGGGAAGGACATTACGGAGCGCCTCATCCTCCCCAGGTTCTGCGAGATGTGCTGTGACTGTCGAATGTTTCATGTCCGGAAGGTCTGCGCTGCCAATTTTGGAGATATTTGCAGTGTAGTTGGCCAACAAGCAACAGAAGAAATGTTGCTGCCCAGGTTCTTCCAGCTGTGCTCTGATAACGTGTGGGGCGTCCGAAAGGCCTGTGCTGAGTGCTTCATGGCTGTCTCCTGTGCAACATGTCAAGAAATCCGACGGACAAAGTTATCAGCACTATTTATTAACTTGATCAGTGATCCTTCACGTTGGGTTCGCCAAGCAGCCTTTCAGTCTCTGGGGCCTTTCATATCCACGTTTGCTAATCCATCAAGCTCGGGCCAGTGCTTTAAAGATGAGAGCAAGAACTCAGAAGACTCCTCGGCAGAAGACAAAGACAGGATGAGAGACAATGATGTCGTAGAAGAAGAGCATCGCAGGCCAGAGGACGCTCCTTCAGACCTCAGTGCCCCTCACTCCAGCGCCAGGCTGGAGAGCCTCGAAGGCTGTGCTGCCAAGACACCTGGGCACTCTGCAGGTGACGTGCCTGCTCCAGTGGACAGCTCCTTACTCTGTACTTTGTCCTCAGAGTCTCCTCAGGAAGCAGCTAGCAATGATGAGAATGGTAGAAAGCCTGACACCAACAGCAAGTCTGCGTCCCGGCCAGACGCTGGCACCAGCTCCCCAGAGGCCACTCCCTTAGACCAGGACATGTTCAACTCCTTCCATTTCTGGAGGACTCCTCTACCTAAAATAGATCTTGATAAAGAGCTCCAGCAGGACCCCGAGGAGAGACTCAGCCCAGAGAGAACAGGAGATGTACCTGCAGCCCCTCTACCAGGCCCTCCCAATATCACCATGGCTACCCGGAAGGAACTAGAAGAAATGATAGAAAACCTTGAGCCACACATGGATGACCCGGATGTGAAAGCACAGGTGGACGTGCTGTCGGCTGCCCTGCGAGCTTCCAGCCTGGATGCTCACGAAGAGACTGGTGGTGTAGAGCAGCGGAGTGAGCTACAAGATGAAGTGTGTGTCAGTGAGCTTCCAGACTGTAACATAAGTCACGACACTTGTGTGCCTTTGATCAGCGCTGCTGAGGAGAATGCGGAGGCCACTCCTGATTATGTCCATGGAGGTGCAGACGTAAGCCCTGGTGATGGCTTCAGCCCGGATGAAGATAGGAGACCCAAAGTCCAGCCCTGGACTTCGTCTCACAAGATGAAATGTTGA
Peptide sequence:
MLTPLGRLDKYAASENVFNRQMVARSLLDTLREVCDDERDCIAVLERISRLADDSEPTVRAELMEQVPHIALFCQENRPSIPYAFSKYLLPIVVRYLADQNNQVRKTSQAALLALLEQELIERFDVETKVCPVLIDLTAPDSNDDVKTEAVAIMCKMAPMVGKDITERLILPRFCEMCCDCRMFHVRKVCAANFGDICSVVGQQATEEMLLPRFFQLCSDNVWGVRKACAECFMAVSCATCQEIRRTKLSALFINLISDPSRWVRQAAFQSLGPFISTFANPSSSGQCFKDESKNSEDSSAEDKDRMRDNDVVEEEHRRPEDAPSDLSAPHSSARLESLEGCAAKTPGHSAGDVPAPVDSSLLCTLSSESPQEAASNDENGRKPDTNSKSASRPDAGTSSPEATPLDQDMFNSFHFWRTPLPKIDLDKELQQDPEERLSPERTGDVPAAPLPGPPNITMATRKELEEMIENLEPHMDDPDVKAQVDVLSAALRASSLDAHEETGGVEQRSELQDEVCVSELPDCNISHDTCVPLISAAEENAEATPDYVHGGADVSPGDGFSPDEDRRPKVQPWTSSHKMKC
IRESfinder result
IRESfinder score
0.352959581
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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