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mmu_ciPtpn4_1874
Basic information of circular RNA
PanCircBase ID:
mmu_ciPtpn4_1874
mm39_Chr. Position ID:
chr1|119647719|119649593|-
Gene name:
Ptpn4
Transcript:
ENSMUST00000064091.12
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
12
Exon/intron offsets:
0
Genomic length:
1874
Exon/intron sizes in nt:
1874
Flanking exon/introns:
chr1:119643745-119649593
Splice length:
1874
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTACTACTTCTATACTATTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTCGTTACCTTTAGATTAGAGGTCTAGGTTTAGAGAGATGGCTCACAGGTTAAGAGTACTGGCTTTTCTTCTAGAAGGATGCAAGTTTAATTCCTAGCACCCACATGGCATCTTACAGCTGTGTGTAACTCCAGTTCCTGGGAAATCCATCATTCTTTTCTTGCCCCCACAAGCACTGGGCCTGGATATGGTATGAAAGACAAATGCACACAGAGATAAGAGGAACCAATTAAAGAGATACAGATACAAAGCAATATAATCATGGTTAGTTGCAAAACCTACTGAGTCAAAATCCCCATAGCATTCTTGTCTGTGTGTCTGTATCAGTAAGTCTATGATGTCTTGTGATGCACACTAGATTTGATAACCCATGCCGTAGGTTGCAATGTATTTTGTAAATAATTTGCCATATTTGCATAGTTTAATCCCAATAGATTTTATAATTCCTAATGCATTTATTATTTGCATGAAAACATTTCTATAAGATATATTCATTTCTTTTATAAAAGCCAAGATATATTTTACATAGTATAAAATTTTTTGTTTAAAAAATTCACAGTTTAACATTTTGTAGAGCTCTCTCCCCTGAGTTCAAAATAACCATTATGCAAATAGGCAAAAAGTTGAATTTGTTGAGTAATAACCACAGATCCTGACATTTTCCTGTATTCTCTTCATTCTGTCTATAATACAGCATAAATTTTGAGAAGTAACTTTAACTAAAGTTAACCCTTAAATTTTTCCTTTATTTTATGTATATTTTTTTCCATTTTGTTTGTTTGTTTGTTTGTTTTTGTTTTGTTTTTTTGTTTTTTCTGTGTGTATATCTGTGCATCATGTGTGTGCAATGTTCATGATGCTGGGAGAGATACCTTATGTTTGGAAGTATAGATAGTTAGAAGTGCTAGTATGGGTGCTGGGAATCAAATCTGCTTCCTTGAGAAGAGCAGTCAGTATTCTAAACTGCTGAGCTATCTCTCTAGTCCCCCTAAATTTGTTTGACTTGCTCTCTTTAAGTTTTTTTACTGTTACATAATTAGGTACGGTTTGGCCTTAACATATATTGCAATATGTAATCACCAGATATATCCACAGCTTCAGATGTGCATCATGTCCTTGTGGTGAGAATGTTCTTAACTCTCTCTACTACGTAATTTGAAATTTACAACTGTTAATCACAGTTGATCTTCTGTGCTACAGAATATGAGAAATTATTTTACCTATTCGCTGTGCCTTTTGCCATTTATTGATTTTTTTTCAATACTCCCCATGGCAACAATTTTTGGGAAATAATTATTTGTAGAAACCTTGATTAGTCCTATCTGTAAATTCTAAAATGACACATAAAAGTTAGTTTTAAAGTGGAATCTAGTAAGACTTACACAGAAAAAGTTACAGGTGATCTAATGGGCCTTCTTCTGCCTCCCGAGTGCTAAGATTAAATGTGTGCACCACCACCGTCTAGCTGCTTCTTTCATTAATGCTTGTATGGTTTGTCTTTTGATCAGTCTTGTTAGAATCTCATCACATTGGATTATTTTAAAACAACCTATATGCCAAGTAAAATTTTTCTTCAGACTTAAGTAGCTCAGTTCTAAAATGAGATGGGTAGGAAGTGACTGAAAATATTACGCAGCCAAGTTTTGGTTCAAATAAGTTTAGAACCAACATAGTAGACATTATTCAGTATGCAAAAATCTCAAGCATTGTAAGGTCTCTGAATCAGGAGTTAGAGAGTGTTATTCAGTGCTTAAGAGCACTTGCTGCTTTTGCACATGGTGGCTCAGAACTGTCTGTAACTCCAGTGTCAGGGTTCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGCACATGGTGGCTCAGAA
60.18
AGCCATCTCTCTAAACCTAGACCT
60.08
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGCACATGGTGGCTCAGA
60.18
AGCCATCTCTCTAAACCTAGACCT
60.08
149
PCR template sequence:
CTGAATCAGGAGTTAGAGAGTGTTATTCAGTGCTTAAGAGCACTTGCTGCTTTTGCACATGGTGGCTCAGAACTGTCTGTAACTCCAGTGTCAGGGTTCTGTAAGTACTACTTCTATACTATTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTCGTTACCTTTAGATTAGAGGTCTAGGTTTAGAGAGATGGCT
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-124-3p(1), mmu-miR-32-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-19b-3p(1), mmu-miR-322-5p(1), mmu-miR-19a-3p(1), mmu-miR-709(1), mmu-miR-495-3p(1), mmu-miR-434-3p(1), mmu-miR-384-3p(1), mmu-miR-129-5p(1), mmu-miR-539-5p(1), mmu-miR-3065-5p(1), mmu-miR-338-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGTCAGGGTTCTGTAAGTACTACTT
siRNA sets
TAGTACTTACAGAACCCTG, AAGTAGTACTTACAGAACC, ACTTACAGAACCCTGACAC
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
0.921009865
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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