top of page
mmu_circPtprn_781
Basic information of circular RNA
PanCircBase ID:
mmu_circPtprn_781
mm39_Chr. Position ID:
chr1|75233486|75235281|-
Gene name:
Ptprn
Transcript:
ENSMUST00000027404.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
8,7,6,5
Exon/intron offsets:
0,450,1102,1536
Genomic length:
1795
Exon/intron sizes in nt:
38,132,352,259
Flanking exon/introns:
chr1:75232545-75233486|chr1:75235281-75237214
Splice length:
781
Other database IDs:
circBase: mmu_circ_0008955, CIRCpedia: MMU_CIRCpedia_29017, circAtlas: mmu-Ptprn_0003
Human Ortholog IDs:
Mature spliced Sequence:
GTCTGGTTTGGTGCCCAGGAAACCAGGCCCTGCAGGGGAATTGCTAACTCAGGGCAATCCTACTGGCTCCTCTCCTGCTGCCCAGGGCTTTCCAAGGCCTGCAGGGGGTGGGGACGGAGCTGGGGCGGGCTCCCCACTGTCCTCTCTGCAGGCTGAGTTGTTACCCCCTCTCTTGGAGCATCTGCTAATGCCCCCACAGCCTCCACACCCTGCTCTGACCTATGAACCTGCACTGCTACAGCCTTACCTCTTCCACCAGTTTGGCTCCCGAGATGGCTCCCGGGGCTCAGAGAGCTCCTCTGGGGTAGTTGGTGTTGGTCACCTGTCCAAGGCTGAAGGTCCTGCACTCTTCAGCAGAAGTGCCTCCAAGGCCATTTTGGGGACTCACTCTGGACACTCTTTTGGGGACCTTACAGGTCCCTCACCTGCTCAACTTTTCCAAGATTCAGGGCTGCTCTACATGGCCCAAGAGTTGCCAGTGCCTGGCAGAGCCCGGGCACCAAGGTTGCCAGAGAATGGGGGCAACAGGGCAGAGGACTCTTCAGAGGGCCATGAGGAGGAAGTACTAGGGGGTCGTGGGGAGAAGTCCCCTCCCCAAGCAGCACAACCAGAATTGAGTCTGCAGAGATTGACTGCTGTACTGGCAGGCTATGGAGTAGAGCTGCGTCAGTTGACCCCGGAGCAGTTTTCTACCCTCTTGACCCTGCTGCAGTTGCTGCCCAAGGGCACAGGAAGAAATCTTGAAGGGGCTGTAAATGTTGGAGGAGCCGATGTCAAGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTCTTGACCCTGCTGCAGTT
60.25
GAGGAGCCAGTAGGATTGCC
59.89
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAAGGGCACAGGAAGAAA
60.18
CAGGAGAGGAGCCAGTAGGA
59.74
140
PCR template sequence:
GCAGTTTTCTACCCTCTTGACCCTGCTGCAGTTGCTGCCCAAGGGCACAGGAAGAAATCTTGAAGGGGCTGTAAATGTTGGAGGAGCCGATGTCAAGAAAGTCTGGTTTGGTGCCCAGGAAACCAGGCCCTGCAGGGGAATTGCTAACTCAGGGCAATCCTACTGGCTCCTCTCCTGCTGCCCAGGGCTTTCCAAGGCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-328-3p(1), mmu-miR-214-3p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
CGATGTCAAGAAAGTCTGGTTTGGTG
siRNA sets
AAACCAGACTTTCTTGACA, AACCAGACTTTCTTGACAT, CAAACCAGACTTTCTTGAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPTPRN_781_ORF_1
0.942
0.182109985
0.954362062
807
ORF sequence:
ATGTTGGAGGAGCCGATGTCAAGAAAGTCTGGTTTGGTGCCCAGGAAACCAGGCCCTGCAGGGGAATTGCTAACTCAGGGCAATCCTACTGGCTCCTCTCCTGCTGCCCAGGGCTTTCCAAGGCCTGCAGGGGGTGGGGACGGAGCTGGGGCGGGCTCCCCACTGTCCTCTCTGCAGGCTGAGTTGTTACCCCCTCTCTTGGAGCATCTGCTAATGCCCCCACAGCCTCCACACCCTGCTCTGACCTATGAACCTGCACTGCTACAGCCTTACCTCTTCCACCAGTTTGGCTCCCGAGATGGCTCCCGGGGCTCAGAGAGCTCCTCTGGGGTAGTTGGTGTTGGTCACCTGTCCAAGGCTGAAGGTCCTGCACTCTTCAGCAGAAGTGCCTCCAAGGCCATTTTGGGGACTCACTCTGGACACTCTTTTGGGGACCTTACAGGTCCCTCACCTGCTCAACTTTTCCAAGATTCAGGGCTGCTCTACATGGCCCAAGAGTTGCCAGTGCCTGGCAGAGCCCGGGCACCAAGGTTGCCAGAGAATGGGGGCAACAGGGCAGAGGACTCTTCAGAGGGCCATGAGGAGGAAGTACTAGGGGGTCGTGGGGAGAAGTCCCCTCCCCAAGCAGCACAACCAGAATTGAGTCTGCAGAGATTGACTGCTGTACTGGCAGGCTATGGAGTAGAGCTGCGTCAGTTGACCCCGGAGCAGTTTTCTACCCTCTTGACCCTGCTGCAGTTGCTGCCCAAGGGCACAGGAAGAAATCTTGAAGGGGCTGTAAATGTTGGAGGAGCCGATGTCAAGAAA
Peptide sequence:
MLEEPMSRKSGLVPRKPGPAGELLTQGNPTGSSPAAQGFPRPAGGGDGAGAGSPLSSLQAELLPPLLEHLLMPPQPPHPALTYEPALLQPYLFHQFGSRDGSRGSESSSGVVGVGHLSKAEGPALFSRSASKAILGTHSGHSFGDLTGPSPAQLFQDSGLLYMAQELPVPGRARAPRLPENGGNRAEDSSEGHEEEVLGGRGEKSPPQAAQPELSLQRLTAVLAGYGVELRQLTPEQFSTLLTLLQLLPKGTGRNLEGAVNVGGADVKK
IRESfinder result
IRESfinder score
0.51261103
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page