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mmu_circPpp4r1_1138
Basic information of circular RNA
PanCircBase ID:
mmu_circPpp4r1_1138
mm39_Chr. Position ID:
chr17|66118237|66131784|+
Gene name:
Ppp4r1
Transcript:
ENSMUST00000073104.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
6,7,8,9,10,11
Exon/intron offsets:
0,2215,2445,3063,4680,13017
Genomic length:
13547
Exon/intron sizes in nt:
14,71,08,66,15,91,28,500
Flanking exon/introns:
chr17:66117675-66118237|chr17:66131784-66136369
Splice length:
1138
Other database IDs:
circAtlas: mmu-Ppp4r1_0024
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGGAAAACCAGTCAGGCAGCTTTGCTGGCTCTGCTGGAGCAGGAACTGATTGAGCGATTTGACGTGGAGACCAAGGTGTGCCCTGTCCTCATAGACCTGACTGCCCCAGACAGCAATGATGATGTGAAGACAGAAGCTGTGGCTATAATGTGCAAGATGGCCCCCATGGTTGGGAAGGACATTACGGAGCGCCTCATCCTCCCCAGGTTCTGCGAGATGTGCTGTGACTGTCGAATGTTTCATGTCCGGAAGGTCTGCGCTGCCAATTTTGGAGATATTTGCAGTGTAGTTGGCCAACAAGCAACAGAAGAAATGTTGCTGCCCAGGTTCTTCCAGCTGTGCTCTGATAACGTGTGGGGCGTCCGAAAGGCCTGTGCTGAGTGCTTCATGGCTGTCTCCTGTGCAACATGTCAAGAAATCCGACGGACAAAGTTATCAGCACTATTTATTAACTTGATCAGTGATCCTTCACGTTGGGTTCGCCAAGCAGCCTTTCAGTCTCTGGGGCCTTTCATATCCACGTTTGCTAATCCATCAAGCTCGGGCCAGTGCTTTAAAGATGAGAGCAAGAACTCAGAAGACTCCTCGGCAGAAGACAAAGACAGGATGAGAGACAATGATGTCGTAGAAGAAGAGCATCGCAGGCCAGAGGACGCTCCTTCAGACCTCAGTGCCCCTCACTCCAGCGCCAGGCTGGAGAGCCTCGAAGGCTGTGCTGCCAAGACACCTGGGCACTCTGCAGGTGACGTGCCTGCTCCAGTGGACAGCTCCTTACTCTGTACTTTGTCCTCAGAGTCTCCTCAGGAAGCAGCTAGCAATGATGAGAATGGTAGAAAGCCTGACACCAACAGCAAGTCTGCGTCCCGGCCAGACGCTGGCACCAGCTCCCCAGAGGCCACTCCCTTAGACCAGGACATGTTCAACTCCTTCCATTTCTGGAGGACTCCTCTACCTAAAATAGATCTTGATAAAGAGCTCCAGCAGGACCCCGAGGAGAGACTCAGCCCAGAGAGAACAGGAGATGTACCTGCAGCCCCTCTACCAGGCCCTCCCAATATCACCATGGCTACCCGGAAGGAACTAGAAGAAATGATAGAAAACCTTGAGCCACACATGGATGACCCGGATGTGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TATCACCATGGCTACCCGGA
60.11
CACCTTGGTCTCCACGTCAA
59.89
161
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGGCCCTCCCAATATCACC
59.89
CACCTTGGTCTCCACGTCAA
59.89
174
PCR template sequence:
CCTCTACCAGGCCCTCCCAATATCACCATGGCTACCCGGAAGGAACTAGAAGAAATGATAGAAAACCTTGAGCCACACATGGATGACCCGGATGTGAAAGGTGAGGAAAACCAGTCAGGCAGCTTTGCTGGCTCTGCTGGAGCAGGAACTGATTGAGCGATTTGACGTGGAGACCAAGGTGTGCCCTGTCCTCATAGACC
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-322-5p(1), mmu-miR-19a-3p(1), mmu-miR-138-5p(1), mmu-miR-139-5p(1), mmu-miR-351-5p(1), mmu-miR-370-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCGGATGTGAAAGGTGAGGAAAACCA
siRNA sets
TTTCCTCACCTTTCACATC, TTCCTCACCTTTCACATCC, TTTTCCTCACCTTTCACAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPP4R1_1138_ORF_1
0.8934
0.245037347
0.992614237
1044
ORF sequence:
ATGTGCAAGATGGCCCCCATGGTTGGGAAGGACATTACGGAGCGCCTCATCCTCCCCAGGTTCTGCGAGATGTGCTGTGACTGTCGAATGTTTCATGTCCGGAAGGTCTGCGCTGCCAATTTTGGAGATATTTGCAGTGTAGTTGGCCAACAAGCAACAGAAGAAATGTTGCTGCCCAGGTTCTTCCAGCTGTGCTCTGATAACGTGTGGGGCGTCCGAAAGGCCTGTGCTGAGTGCTTCATGGCTGTCTCCTGTGCAACATGTCAAGAAATCCGACGGACAAAGTTATCAGCACTATTTATTAACTTGATCAGTGATCCTTCACGTTGGGTTCGCCAAGCAGCCTTTCAGTCTCTGGGGCCTTTCATATCCACGTTTGCTAATCCATCAAGCTCGGGCCAGTGCTTTAAAGATGAGAGCAAGAACTCAGAAGACTCCTCGGCAGAAGACAAAGACAGGATGAGAGACAATGATGTCGTAGAAGAAGAGCATCGCAGGCCAGAGGACGCTCCTTCAGACCTCAGTGCCCCTCACTCCAGCGCCAGGCTGGAGAGCCTCGAAGGCTGTGCTGCCAAGACACCTGGGCACTCTGCAGGTGACGTGCCTGCTCCAGTGGACAGCTCCTTACTCTGTACTTTGTCCTCAGAGTCTCCTCAGGAAGCAGCTAGCAATGATGAGAATGGTAGAAAGCCTGACACCAACAGCAAGTCTGCGTCCCGGCCAGACGCTGGCACCAGCTCCCCAGAGGCCACTCCCTTAGACCAGGACATGTTCAACTCCTTCCATTTCTGGAGGACTCCTCTACCTAAAATAGATCTTGATAAAGAGCTCCAGCAGGACCCCGAGGAGAGACTCAGCCCAGAGAGAACAGGAGATGTACCTGCAGCCCCTCTACCAGGCCCTCCCAATATCACCATGGCTACCCGGAAGGAACTAGAAGAAATGATAGAAAACCTTGAGCCACACATGGATGACCCGGATGTGAAAGGTGAGGAAAACCAGTCAGGCAGCTTTGCTGGCTCTGCTGGAGCAGGAACTGATTGA
Peptide sequence:
MCKMAPMVGKDITERLILPRFCEMCCDCRMFHVRKVCAANFGDICSVVGQQATEEMLLPRFFQLCSDNVWGVRKACAECFMAVSCATCQEIRRTKLSALFINLISDPSRWVRQAAFQSLGPFISTFANPSSSGQCFKDESKNSEDSSAEDKDRMRDNDVVEEEHRRPEDAPSDLSAPHSSARLESLEGCAAKTPGHSAGDVPAPVDSSLLCTLSSESPQEAASNDENGRKPDTNSKSASRPDAGTSSPEATPLDQDMFNSFHFWRTPLPKIDLDKELQQDPEERLSPERTGDVPAAPLPGPPNITMATRKELEEMIENLEPHMDDPDVKGEENQSGSFAGSAGAGTD
IRESfinder result
IRESfinder score
0.373198254
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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