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mmu_ciPtpn13_2153
Basic information of circular RNA
PanCircBase ID:
mmu_ciPtpn13_2153
mm39_Chr. Position ID:
chr5|103739219|103741372|+
Gene name:
Ptpn13
Transcript:
ENSMUST00000048957.11
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
45
Exon/intron offsets:
0
Genomic length:
2153
Exon/intron sizes in nt:
2153
Flanking exon/introns:
chr5:103739219-103741372
Splice length:
2153
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTCAGTCACTCGTCAGAAAGCAGACCTGCACGCTCTCCGGGAGGCCACAACAAAAGCAGGGCATCTACTATCTTTTATTTTTGAGACCAGGTCTCACGTAGCCCAGACTGGCCTCAAAGTCATTATACAGCTACAACAACCTGGAAGTCCTGATCCCCCTGCTTCTGTCTCCTGGGTACTGGGATTACAGGAATGTGTGATCCTGTCAAACCACACGCAGCTTCCAGTAGAGTTTTAAGAGTGGCCCTCATTCAGTTTCATCTGGTAGATGCTGTATTAGAACAAACATGGGGTTTTAACATGATCATCAGTCTGTGCTTAGGAATAAACAGCACAAAACAGTTCATAAACTGCAGTGTACATAGAACCATTACTGTTGTTGTTATTATTATTGTTGTTGTTTTTTTTCGGGATAAGGTTTCCCTGTGTAGCCCTGGCTGTCCTGGAACTCGATCTGTAGACCAGGCTAAGCTGGCCTTGAACTCTAGATTGGCCTACTTCTGGTTGCCAAGTGCTGGGATTAAAGGCATGTGCCAGCACACCTGATGAAACTTGCTTTGTTTAACACCTACAGGGTCCAATATCTAAGTAGACTAATTGAAGCTGTTTTAAGAAATCTGTGGCTATGAGAACACGTCCGGTGAAGGCAGCCTACATGTTTAGCGGGTGTGCACAGCTGTGCCATATCAGCTGTCATTGACACACTTGCCAGACACACTGGATAAAACTAGTGCATGCTAGCTTGTGATCGGCCTTTAGACAGAGCCAGCCGTCTGTCTCTTCAGTGTGGCATTCCCTCACCTGGTGCACCCTTCCCGGAAATATGAGCTATGCAAAGCCATGTTTGCTCATGAGTCTTTAACTTTCTTCAACGTTTCTTTGTTTTTCCTTCTCTGTGTGTATATGTGTTTGTGTGTGTACATAGATGTGTAGGTATGTCTGTGCGCACGTGTACGCTAGAGGCTGATGTAGGAATCTTCCTTCCTCTGTGGCTCTCTGCCTCCCTTGAGAAAGACTCGGCCACTGAACACGGAGCTCCCAGATTGAACTGCTCCGGCTGCCTTCCAGCCCCAGGAATCCTCCTGACTCCATCTCCCCAGCACAGGATTAAAGGGCAGTCCCCATGCCCAACTTTTTCTGTGGATGCTGGGGATGCAAGCTCAGACTCCATGCTTATGTGACAAGCACTTTACCCCTGAGCTTTCTTCAGCTTTTCTAGAAGGAAAACAAAACAAAACAAAAACAAAACAGTATGCTGATTCACTTCCATTGGCGACATATAAACGTGTTATGAGACTTTCCTTATTATTTACAAAGTGTCAGAGCTTTTATTCCTTTATGAAACCTAAACATTTTAGTTAACACATTTTAATTAATGCTCCTAGGTCCTGCCAGGTGATGTTTTGGCTCACACGAGCTTACCCATTGCTCAGATGAGCTTAGCACTTCGTGTTCCTCAGGTGACCTGATCATGAATCACAGTAGAGTAGTCCAACTCAAACCCTGGCATGGACCCCAGGTCCAGCATTTTAACAACAGGCAGACAGCCGTTCAGTACCCACATGGAGCTTGCTGCCTGCGTGGGCGTGGGCTGGCTGTGTTAGTCGTGCTGCTGGGAAAACAAAACCGAAAGGAAGGGTTGCTGGACTCTGAGATACAGGCTGTGTGTTCAACAACACAGGATGGCCTGAGAGGCTGCATTTGAGGAAAACGAAGCAGATAATAAAACCAGAGGATGCTGGGGGAGGAGGAGTTCTAATGGGAAAGAAAGAATAAAGTTCTGAGACTGACATTGCCAAACATATCACTTAAATGAGCCCACAGAGGCCTGGGTACCATCCCTAGCCACTAGGACTGGGCGGTGGTGATGCAGTCCGTGTATTTTTCAATCTGTTGTTGTCGGTTTTAGCCACAGTCTTGCTCTGTACCCTAAGCTGGCCTTGAATACTCCGTCCTCCTCTCTTGGTCTGAATACTGGAAATTAGGCATATGCCACCATACCCAGCTTTGTATGTTTATACCTTTTTATCTCTTCCATTTTTTCTTTTGATCTGATTCAATATACCACTCAAATTTGAAAGATGGAAATGATACTGTAAGGACCTGACTTAGGGACAGGTGACATTGTAACTCACTACATTTTACACTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTCAAATTTGAAAGATGGA
56.61
CTGCTTTTGTTGTGGCCTCC
59.97
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCACTCAAATTTGAAAGATGGA
56.61
CCTGCTTTTGTTGTGGCCTC
59.97
150
PCR template sequence:
GATTCAATATACCACTCAAATTTGAAAGATGGAAATGATACTGTAAGGACCTGACTTAGGGACAGGTGACATTGTAACTCACTACATTTTACACTTTCAGGTCAGTCACTCGTCAGAAAGCAGACCTGCACGCTCTCCGGGAGGCCACAACAAAAGCAGGGCATCTACTATCTTTTATTTTTGAGACCAGGTCTCACGTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
29
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-16-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-199a-5p(1), mmu-miR-135a-5p(1), mmu-miR-298-5p(1), mmu-miR-216a-5p(1), mmu-miR-217-5p(1), mmu-miR-184-3p(1), mmu-miR-709(1), mmu-miR-203-3p(1), mmu-miR-320-3p(1), mmu-miR-324-5p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-149-5p(1), mmu-miR-433-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-676-3p(1), mmu-miR-182-5p(1), mmu-miR-340-5p(1), mmu-miR-466d-3p(1), mmu-miR-190b-5p(1), mmu-miR-532-5p(1), mmu-miR-466b-3p(1), mmu-miR-574-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTACACTTTCAGGTCAGTCACTCGT
siRNA sets
AGTGACTGACCTGAAAGTG
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
0.787097674
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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