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mmu_circPpargc1a_1262
Basic information of circular RNA
PanCircBase ID:
mmu_circPpargc1a_1262
mm39_Chr. Position ID:
chr5|51629939|51647587|-
Gene name:
Ppargc1a
Transcript:
ENSMUST00000132734.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
10,9,8,7,6
Exon/intron offsets:
0,281,898,17419,17602
Genomic length:
17648
Exon/intron sizes in nt:
121,105,916,74,46
Flanking exon/introns:
chr5:51620669-51629939|chr5:51647587-51651942
Splice length:
1262
Other database IDs:
circAtlas: mmu-Ppargc1a_0026
Human Ortholog IDs:
Mature spliced Sequence:
CCAAACCAACAACTTTATCTCTTCCTCTGACCCCAGAGTCACCAAATGACCCCAAGGGTTCCCCATTTGAGAACAAGACTATTGAGCGAACCTTAAGTGTGGAACTCTCTGGAACTGCAGGCCTAACTCCTCCCACAACTCCTCCTCATAAAGCCAACCAAGATAACCCTTTCAAGGCTTCGCCAAAGCTGAAGCCCTCTTGCAAGACCGTGGTGCCACCGCCAACCAAGAGGGCCCGGTACAGTGAGTGTTCTGGTACCCAAGGCAGCCACTCCACCAAGAAAGGGCCCGAGCAATCTGAGTTGTACGCACAACTCAGCAAGTCCTCAGGGCTCAGCCGAGGACACGAGGAAAGGAAGACTAAACGGCCCAGTCTCCGGCTGTTTGGTGACCATGACTACTGTCAGTCACTCAATTCCAAAACGGATATACTCATTAACATATCACAGGAGCTCCAAGACTCTAGACAACTAGACTTCAAAGATGCCTCCTGTGACTGGCAGGGGCACATCTGTTCTTCCACAGATTCAGGCCAGTGCTACCTGAGAGAGACTTTGGAGGCCAGCAAGCAGGTCTCTCCTTGCAGCACCAGAAAACAGCTCCAAGACCAGGAAATCCGAGCGGAGCTGAACAAGCACTTCGGTCATCCCTGTCAAGCTGTGTTTGACGACAAATCAGACAAGACCAGTGAACTAAGGGATGGCGACTTCAGTAATGAACAATTCTCCAAACTACCTGTGTTTATAAATTCAGGACTAGCCATGGATGGCCTATTTGATGACAGTGAAGATGAAAGTGATAAACTGAGCTACCCTTGGGATGGCACGCAGCCCTATTCATTGTTCGATGTGTCGCCTTCTTGCTCTTCCTTTAACTCTCCGTGTCGAGACTCAGTGTCACCACCGAAATCCTTATTTTCTCAAAGACCCCAAAGGATGCGCTCTCGTTCAAGATCCTTTTCTCGACACAGGTCGTGTTCCCGATCACCATATTCCAGGTCAAGATCAAGGTCCCCAGGCAGTAGATCCTCTTCAAGATCCTGTTACTACTATGAATCAAGCCACTACAGACACCGCACACACCGCAATTCTCCCTTGTATGTGAGATCACGTTCAAGGTCACCCTACAGCCGTAGGCCCAGGTACGACAGCTATGAAGCCTATGAGCACGAAAGGCTCAAGAGGGATGAATACCGCAAAGAGCACGAGAAGCGGGAGTCTGAAAGGGCCAAACAGAGAGAGAGGCAGAAGCAGAAAGCAATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGCACGAAAGGCTCAAGAGG
60.32
TTGGTGACTCTGGGGTCAGA
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CACGAAAGGCTCAAGAGGGA
59.68
TTGGTGACTCTGGGGTCAGA
60.11
141
PCR template sequence:
TGAGCACGAAAGGCTCAAGAGGGATGAATACCGCAAAGAGCACGAGAAGCGGGAGTCTGAAAGGGCCAAACAGAGAGAGAGGCAGAAGCAGAAAGCAATTCCAAACCAACAACTTTATCTCTTCCTCTGACCCCAGAGTCACCAAATGACCCCAAGGGTTCCCCATTTGAGAACAAGACTATTGAGCGAACCTTAAGTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-210-3p(1), mmu-miR-375-3p(1), mmu-miR-328-3p(1), mmu-miR-196a-5p(1), mmu-miR-324-5p(1), mmu-miR-125b-5p(1), mmu-miR-381-3p(1), mmu-miR-431-5p(1), mmu-miR-351-5p(1), mmu-miR-199b-3p(1), mmu-miR-194-5p(1), mmu-miR-199a-3p(1), mmu-miR-382-5p(1), mmu-miR-705(1), mmu-miR-1187(1), mmu-miR-190b-5p(1), mmu-miR-1199-5p(1), mmu-miR-540-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAGAAAGCAATTCCAAACCAACAAC
siRNA sets
GTTGTTGGTTTGGAATTGC, TTGTTGGTTTGGAATTGCT, TTGGTTTGGAATTGCTTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPPARGC1A_1262_ORF_1
0.9709
0.092292332
0.670985475
531
ORF sequence:
ATGGATGGCCTATTTGATGACAGTGAAGATGAAAGTGATAAACTGAGCTACCCTTGGGATGGCACGCAGCCCTATTCATTGTTCGATGTGTCGCCTTCTTGCTCTTCCTTTAACTCTCCGTGTCGAGACTCAGTGTCACCACCGAAATCCTTATTTTCTCAAAGACCCCAAAGGATGCGCTCTCGTTCAAGATCCTTTTCTCGACACAGGTCGTGTTCCCGATCACCATATTCCAGGTCAAGATCAAGGTCCCCAGGCAGTAGATCCTCTTCAAGATCCTGTTACTACTATGAATCAAGCCACTACAGACACCGCACACACCGCAATTCTCCCTTGTATGTGAGATCACGTTCAAGGTCACCCTACAGCCGTAGGCCCAGGTACGACAGCTATGAAGCCTATGAGCACGAAAGGCTCAAGAGGGATGAATACCGCAAAGAGCACGAGAAGCGGGAGTCTGAAAGGGCCAAACAGAGAGAGAGGCAGAAGCAGAAAGCAATTCCAAACCAACAACTTTATCTCTTCCTCTGA
Peptide sequence:
MDGLFDDSEDESDKLSYPWDGTQPYSLFDVSPSCSSFNSPCRDSVSPPKSLFSQRPQRMRSRSRSFSRHRSCSRSPYSRSRSRSPGSRSSSRSCYYYESSHYRHRTHRNSPLYVRSRSRSPYSRRPRYDSYEAYEHERLKRDEYRKEHEKRESERAKQRERQKQKAIPNQQLYLFL
IRESfinder result
IRESfinder score
0.466469908
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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