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mmu_ciPtpn4_2264
Basic information of circular RNA
PanCircBase ID:
mmu_ciPtpn4_2264
mm39_Chr. Position ID:
chr1|119607949|119610213|-
Gene name:
Ptpn4
Transcript:
ENSMUST00000064091.12
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
22
Exon/intron offsets:
0
Genomic length:
2264
Exon/intron sizes in nt:
2264
Flanking exon/introns:
chr1:119607925-119610213
Splice length:
2264
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTTTTTTGTTCTGCCTTTGTTGTTGGGAGCAATTGAAAACCATTGTAAATTTGAAGGTTAATTCCTTTTTATTGAAAGTCTAACCTTGATTCTTTGTGCAATTGATGAACGAGGTAATAGTGAATCATCATTACTAGGGCAAATATGTAGTTAGGTGTTTATAAGTAAATAGTCACATTTCATCAGCTAATCAATGCACAGCTTCATTTAAAGCTTTATTTAATAATAACATTGTTGTTTTGTTAACTTTGCATAGCCAATAGCATTTGAAGTGTAATTCATGACTGAAGAAAGCTAATCTACATTCTCTCCATGGTGAATAACATTGCAACCTTCATGTACATAAGAACTCTATACAGCACTTCATCACTGTGATTGTAAATGGTGCAATTACCCACAATAAACCTGAAAATGTGAAGAATATGGTACTGCACAGTAATCGGGGCTGCATGTAGGCAGTATAAAAGGGGAATGAAACAGCTGCCTTTTGATGTCATCTGAAAAAAAAATGCTTATCCAGTGACTCAAATGGTTTCTTCCTCAGTATGCCTAGACATAATCAACAAAGCCCGCCTCCTGTTTTGAAACTGCATAAGAACTTTAGCAATTATGGAGGCTAGAGAGATGGCAAAGCAGTTAAGCTTGCTGCATAATCATGAGGCCCCTTCTTCAAAGGATTAGGCAGAGAGTGATATAAGTTGCCATACAGCTCCTCCTTTTGGCCTTAGATAATGACTTGTGGAGTTGTTGTTTGTTTGTTTTTTTAAGCAAAGCCAGGATAATGAAACTTAGAAAAATAAGTATCACAGTTAAATGAAGTTTAAACTTAGAAAACAAAGTACAAATTTAAACTACATAAAAGTTCTACTGTTTATCTCTGAAAATGAAAGGCCAAAAATTTGATGATAACATACACGTGTATAGTTCTTTATCTGAAACCTTCAAGTATTCATTGGCATTGAAAATTTTTAGATTTTTTTAAGACTATTCAGTGCGTGTAGCAGTGCAATAGGAAGTAAATATTCCTAGCAGGTTATAATAGGGGCCCTTTAATTATTATACTGATACTATATAAATATTCTGAGTGGGATTAAGTCAAAGTCACATTTTGATGTCAAATGCTTTCAAGTAAAGTCACCTTTAAAATGCTTTCAAGTTAGGACAAGGTTCAAAACACCAAAATCAGTTTTTCATTTCAGACTATTGGTCTTTTCAGAACTATGGATAAGGGAATGTAGCTATATTGGCAAGTATCAATTAACTACATTCCTGTGTGTTGTTGGTTAAAATGTAGACTGGTTTCTTTGGGGAGCAGTTTGGTATTGTTAGAAGTTGAACTGTGAATACATTTGTATCCAGCATTTTCATTTCTTCCTGTTGACCTTATAGGTAGATATATTTTTTCGTTTGCTAAAAATGTCAGGTTTAGAGAAGAGCAGGGCTCAGTTTACTTTGCTACTGGTAACAAACATTAACAATGCCTAAAATTTCTGTTTTATAAGTTACAGTATTTTTTTAAGAAGAGTCATTAAAAGAAAGAAATTAGGTACTAATTTGGGTATTATCTTTCAAACAGTGGGATTCAGAACACCATACACATTGTGTTACTCTTTTAAAATTGGTTTTATAGAAAAATAGTTGTTGTATACAGACTATTTATGTGAAAGAGGTACTAGGAAGTAGAAAAACAAATTTACCCTCTGGTAATAAGTGGAAGCTGGTTTGGGAGGGAGACTTCAAGTTTCAAGTACCTTGGGTATTTTCTAAATTGCTATATGTAGGTATCAGCTTGTTGAAATCAACCTCAAATGTAGAGTGTTGATTCCTCTATATTTATTGTCTTATTTCATTCTAAAAACAAACTTTAATATTATTCTAATGGTTCTTCACATTATTTAATGAGCACCATTCAGCTAAAATGAATGGCAGAATTTTTCTTCCTTAGAAAATTTACCAATAAACTATTTATACTTTTAAAAAATATTTTTACAAACTCTTGGTATTTAAAAGAAGTTCCTCTATAATGCTGCCTCTTAAGCCATAATAGTTTGAGATACGGTGGTACATGCCTATAATAGTTCAGATGCTGGGCTACATAGTGAGACCTTGTTTCAAAGAAGAAAAAAATAAAGGAAGGTAGTGTTTGGAAAATATTTGCTTTAAGTTCCTCTTCCACCAATTAAATAATGAATAAGTATAACTTTGGACATTGCCAGGAAATTTCTTTTACAAGTAAAATTATTAATGAAGATCATTTCTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCCTCTTCCACCAATTAAA
55.26
TGGTTTTCAATTGCTCCCAACA
59.23
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGTTCCTCTTCCACCAATTAA
55.26
TGGTTTTCAATTGCTCCCAACA
59.23
145
PCR template sequence:
TAAGTTCCTCTTCCACCAATTAAATAATGAATAAGTATAACTTTGGACATTGCCAGGAAATTTCTTTTACAAGTAAAATTATTAATGAAGATCATTTCTTGTAAGTTTTTTGTTCTGCCTTTGTTGTTGGGAGCAATTGAAAACCATTGTAAATTTGAAGGTTAATTCCTTTTTATTGAAAGTCTAACCTTGATTCTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
25
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(2), mmu-miR-25-3p(2), mmu-miR-363-3p(2), mmu-miR-23b-3p(1), mmu-miR-27a-3p(1), mmu-miR-1a-3p(1), mmu-miR-32-5p(1), mmu-miR-429-3p(1), mmu-miR-206-3p(1), mmu-miR-103-3p(1), mmu-miR-150-5p(1), mmu-miR-221-3p(1), mmu-miR-92a-3p(1), mmu-miR-29b-3p(1), mmu-miR-29c-3p(1), mmu-miR-33-5p(1), mmu-miR-19a-3p(1), mmu-miR-23a-3p(1), mmu-miR-495-3p(1), mmu-miR-128-3p(1), mmu-miR-434-3p(1), mmu-miR-182-5p(1), mmu-miR-107-3p(1), mmu-miR-384-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGATCATTTCTTGTAAGTTTTTTGT
siRNA sets
AAAAACTTACAAGAAATGA, AAACTTACAAGAAATGATC, AAAAAACTTACAAGAAATG
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
0.88893074
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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