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mmu_ciPank3_1834
Basic information of circular RNA
PanCircBase ID:
mmu_ciPank3_1834
mm39_Chr. Position ID:
chr11|35674400|35676234|+
Gene name:
Pank3
Transcript:
ENSMUST00000018990.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
6
Exon/intron offsets:
0
Genomic length:
1834
Exon/intron sizes in nt:
1834
Flanking exon/introns:
chr11:35674400-35676234
Splice length:
1834
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATGTAAACACTTTTTGTGGGTTATTTAACAGTGTGTTTTATATGAAATTGTTCTATATTTCTTTTTGTTTGTTTGTTTGTTTGGTTTGTGTTTTGTTTTTTGTTTTTTTCGAGACACAGTTTCTCTGTAGCCCTGGCTGTCCTGGAACTAATTCTGTAAACCAGGCTGTCCTCGAAACACAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATCAAAGGTGTGCGCCACCACTGCCTGGCTCTATATTTCTATGTATCTTGTATTTATATATGTAAAAATTAAATTATTTTTATGTGTACGTAAGTGGAGACCAGAAGATAACTTCAGGTGTCATCGAAAACACTCTCCACAATCTTTGAGACAGAGTCTCTCGCTGGCATAGAATGTACTAGTGAGGCTCTACTGGCTGGTCTACAAACCCCAGAGATCTGCCTCACCCAGATCTGGGCATACAGAGATGTGCCACCACACTTGGCTTTTTTTTTTTTTTTTAACCCATTTGTTTTAGGAATCAAACCTAGTTCCTTATGTTTACAGATTGAGCTATTTTCCTAGGCCAGGGTCATAAGTCATGTGTTTTGAAAGGTCACACTACACAGCCGGTTCAGACTGAATTTCAGGCCCCCATAAATGATGAAATTACGGGTGTGTGCCACAAATTATTGACTTAAGTAAATTGATTCTTTTTGTTTCAGTTTGGCAGGCAGTTAGCTACCACATAGACAGCTCACAGATGAGAATTTCATTGCTCTTCTAACCGAGTGAACAATAGGAAGTTTCTTGTTTCTCAGATAGAAGATTCTTTTTAATCCCCCCACCCCCCGAAATAACCCTATTGTGAACCCTTGAAATCTGTGCGATTGGTTTTCCTCCTGTTAAGCTTAATGGCTGCACTTGTATCATCCTAAAGCTCAAGGAGGCAGGGCGGGCAAGATGTTTGCTAGCTCCCTGGCCAGGCTGATCCATAGAAGTGCCAGGGTTCCATGGCAAGACCCCATGGCAAACAACACAAAACAAAAACCCAAACAGCCCACCTCCTATGGTTTTTGCTATTCACAATATCCAGTTAAATTCTAATCTGTGCAGTTAATCAGTCTTTTTTTTTTTTTTCATTTGCATGAGTGCTTGCCTGTACAGATGTCTGCCGCATATGTATGCAGTACCCTAGAAGCCCAAGAGAGGGCAGCTGGAACTGGAGTTACAGACGGTTGACAGCTGGGTGGCTGGGTGCTGGGAACTGAACCCCAGCCAGGCATCTGGGAGAACAGACAATGCCTTTCCCCTTCCTCTCTCCCTCTCGCTCCAGCCCTGCTCACTCTGGCCTCCGCTTGCTCCAGGTTTTTTTTTTTTTTTTTATGTTTCTCATTATGGATGGTTGTGAGCTACCTTGTGGTTGCTGGGTTTTGAACTCATGACCTCTGGAAGAGCAGTCAGTGCTCTTAACAGCTAAGCTATCTCTCTAGCCCCCCCCCCTCTTTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTTTCAAGACAGGGTTTCTCTTTAGCCTTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCTCCTGCCTCTAATCAGTCTTCTATGATGAATTCAAATGCTTACATTATTCTGAATTAGGAACAAGGTACTGGCCTTTTGACTCACAGAAATCCACCTTCCTCTGAGTGCTAGAATTTTAGCTGTTGTTTTTATGGGATGTACCCTTTCATATATTAATGTGAAGAAGAAGGCTATATAAATGTGCTCTTACAAATTAATTTAAAAACTACATTGCCTTAAACTGTTTAAAAATCGTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAAGAAGGCTATATAAATGTGCTCT
58.03
ACACAAACCAAACAAACAAACA
56.24
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGAAGGCTATATAAATGTGCTCT
56.79
ACACAAACCAAACAAACAAACA
56.24
170
PCR template sequence:
ACCCTTTCATATATTAATGTGAAGAAGAAGGCTATATAAATGTGCTCTTACAAATTAATTTAAAAACTACATTGCCTTAAACTGTTTAAAAATCGTGCAGGTATGTAAACACTTTTTGTGGGTTATTTAACAGTGTGTTTTATATGAAATTGTTCTATATTTCTTTTTGTTTGTTTGTTTGTTTGGTTTGTGTTTTGTTT
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-134-5p(1), mmu-let-7e-5p(1), mmu-miR-34c-5p(1), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-381-3p(1), mmu-miR-495-3p(1), mmu-miR-30d-5p(1), mmu-miR-494-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-466d-3p(1), mmu-miR-5101(1), mmu-miR-490-3p(1), mmu-miR-99a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAAATCGTGCAGGTATGTAAACACT
siRNA sets
TTTACATACCTGCACGATT, TTACATACCTGCACGATTT, TGTTTACATACCTGCACGA
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
0.899811559
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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