top of page
mmu_circPxn_682
Basic information of circular RNA
PanCircBase ID:
mmu_circPxn_682
mm39_Chr. Position ID:
chr5|115682401|115683864|+
Gene name:
Pxn
Transcript:
ENSMUST00000067268.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,538,1029,1261
Genomic length:
1463
Exon/intron sizes in nt:
2,27,11,61,37,202
Flanking exon/introns:
chr5:115644927-115682401|chr5:115683864-115684871
Splice length:
682
Other database IDs:
circBase: mmu_circ_0012033, CIRCpedia: MMU_CIRCpedia_3851, circAtlas: mmu-Pxn_0008
Human Ortholog IDs:
Mature spliced Sequence:
ATGCCCTGCTGGCAGACTTGGAATCTACCACCTCCCACATCTCCAAACGGCCAGTGTTCTTGTCAGAGGAGCCCCCCTACTCCTACCCAACTGGAAACCACACATACCAGGAGATTGCGGTGCCACCTCCGGTCCCACCACCACCGTCCAGCGAGGCCCTCAATGGCACGGTCCTGGACCCTTTAGATCAGTGGCAGCCTAGTGGTTCCAGATACGCTCACCAGCAGCCTCCGTCCCCACTGCCCGTGTACAGCTCCAGTGCTAAAAATTCCAGTGCCTCCAACACCCAGGACGGCGTGGGCTCCCTTTGTTCCCGAGCAGGCGAGGAAGAGCACGTCTACAGCTTCCCCAACAAGCAGAAGTCGGCAGAGCCCTCACCTACCGTCATGAGCTCCTCCCTGGGCAGCAACCTCTCTGAACTTGACCGGCTGTTACTGGAGCTGAACGCAGTGCAGCACAGCCCGCCTGGCTTCCCTGCAGATGAAGCCGAATCGAGCCCCCCCTTGCCTGGAGCCCTGAGCCCCCTTTATGGCATCCCAGAAAATAACACTCCCTTGGGGGGCAAAGCGGGGCCCCTGGTGAAAGAGAAGCCAAAGCGAAATGGAGGCCGGGGGCTGGAGGATGTGCGGCCCAGCGTGGAGAGCCTCTTGGATGAACTGGAGAGTTCCGTGCCCAGCCCTGT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGGAGAGCCTCTTGGATG
60.18
AGTTGGGTAGGAGTAGGGGG
59.66
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCCAAAGCGAAATGGAGG
59.11
CAAGAACACTGGCCGTTTGG
59.97
157
PCR template sequence:
AAGAGAAGCCAAAGCGAAATGGAGGCCGGGGGCTGGAGGATGTGCGGCCCAGCGTGGAGAGCCTCTTGGATGAACTGGAGAGTTCCGTGCCCAGCCCTGTATGCCCTGCTGGCAGACTTGGAATCTACCACCTCCCACATCTCCAAACGGCCAGTGTTCTTGTCAGAGGAGCCCCCCTACTCCTACCCAACTGGAAACCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-184-3p(1), mmu-miR-138-5p(1), mmu-miR-24-3p(1), mmu-miR-136-5p(1), mmu-miR-676-3p(1), mmu-miR-705(1), mmu-miR-29b-2-5p(1), mmu-miR-1187(1), mmu-miR-1904(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCCAGCCCTGTATGCCCTGCTGGC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPXN_682_ORF_1
1.0084
0.39060654
0.975781493
762
ORF sequence:
ATGGAGGCCGGGGGCTGGAGGATGTGCGGCCCAGCGTGGAGAGCCTCTTGGATGAACTGGAGAGTTCCGTGCCCAGCCCTGTATGCCCTGCTGGCAGACTTGGAATCTACCACCTCCCACATCTCCAAACGGCCAGTGTTCTTGTCAGAGGAGCCCCCCTACTCCTACCCAACTGGAAACCACACATACCAGGAGATTGCGGTGCCACCTCCGGTCCCACCACCACCGTCCAGCGAGGCCCTCAATGGCACGGTCCTGGACCCTTTAGATCAGTGGCAGCCTAGTGGTTCCAGATACGCTCACCAGCAGCCTCCGTCCCCACTGCCCGTGTACAGCTCCAGTGCTAAAAATTCCAGTGCCTCCAACACCCAGGACGGCGTGGGCTCCCTTTGTTCCCGAGCAGGCGAGGAAGAGCACGTCTACAGCTTCCCCAACAAGCAGAAGTCGGCAGAGCCCTCACCTACCGTCATGAGCTCCTCCCTGGGCAGCAACCTCTCTGAACTTGACCGGCTGTTACTGGAGCTGAACGCAGTGCAGCACAGCCCGCCTGGCTTCCCTGCAGATGAAGCCGAATCGAGCCCCCCCTTGCCTGGAGCCCTGAGCCCCCTTTATGGCATCCCAGAAAATAACACTCCCTTGGGGGGCAAAGCGGGGCCCCTGGTGAAAGAGAAGCCAAAGCGAAATGGAGGCCGGGGGCTGGAGGATGTGCGGCCCAGCGTGGAGAGCCTCTTGGATGAACTGGAGAGTTCCGTGCCCAGCCCT
Peptide sequence:
MEAGGWRMCGPAWRASWMNWRVPCPALYALLADLESTTSHISKRPVFLSEEPPYSYPTGNHTYQEIAVPPPVPPPPSSEALNGTVLDPLDQWQPSGSRYAHQQPPSPLPVYSSSAKNSSASNTQDGVGSLCSRAGEEEHVYSFPNKQKSAEPSPTVMSSSLGSNLSELDRLLLELNAVQHSPPGFPADEAESSPPLPGALSPLYGIPENNTPLGGKAGPLVKEKPKRNGGRGLEDVRPSVESLLDELESSVPSP
IRESfinder result
IRESfinder score
0.431166961
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page