top of page
mmu_circAmfr_944
Basic information of circular RNA
PanCircBase ID:
mmu_circAmfr_944
mm39_Chr. Position ID:
chr8|94700686|94712100|-
Gene name:
Amfr
Transcript:
ENSMUST00000053766.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
13,12,11,10,9,8,7
Exon/intron offsets:
0,677,1975,6259,9253,10775,11280
Genomic length:
11414
Exon/intron sizes in nt:
1,85,84,13,51,04,19,11,00,000
Flanking exon/introns:
chr8:94699942-94700686|chr8:94712100-94714001
Splice length:
944
Other database IDs:
circAtlas: mmu-Amfr_0015
CIRCpedia: HSA_CIRCpedia_180691
Human Ortholog IDs:
Mature spliced Sequence:
TTATTTGGCAACATCTGGTTATCTATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGAATTATTTGCGAGTGGTAGGAAACATGGAAGCCAGGTTTGCTGTTGCAACTCCAGAGGAACTAGCTGTCAATAATGATGACTGTGCAATCTGCTGGGACTCCATGCAGGCTGCAAGGAAACTGCCCTGTGGACATCTTTTTCACAACTCCTGCCTTCGTTCTTGGCTAGAACAAGACACCTCTTGTCCAACATGCAGAATGTCTCTTAATATTGCTGATGGCAGTCGTGCCAGGGAAGACCATCAAGGAGAGAACCTGGACGAGAACTTGGTTCCTGTAGCAGCTGCCGAAGGCAGGCCTCGCTTGAACCAGCACAATCACTTCTTCCACTTCGATGGGTCCCGGATTGCAAGCTGGCTGCCAAGTTTTTCAGTTGAAGTGATGCACACTACCAACATTCTTGGCATCACGCAGGCAAGCAACTCTCAGCTAAATGCCATGGCTCATCAGATTCAGGAGATGTTCCCTCAGGTCCCGTACCACCTTGTGCTCCAGGACCTCCAGATGACACGCTCCGTGGAGATAACAACAGATAACATCTTAGAAGGACGGATTCAAGTACCTTTCCCCACGCAGCGGTCGGATAGCCTGAGGCCTGCACTGAACAGCCCAGTGGAGAGGCCCAGCCCTGACCTGGAGGAGGGAGAAGCTTCTGTCCAGACGGAGCGTGTACCACTGGACCTCAGTCCTCGCCTAGAGGAGACCTTGGACTTCAGTGAGGTAGAACTAGAGCCTATTGAGGTGGAAGACTTTGAGGCCCGTGGAAGCCGCTTCTCCAAGTCTGCTGATGAGAGACAGCGCATGTTAGTTCAGCGCAAGGATGACCTCCTGCAGCAGGCTCGAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGCCGCTTCTCCAAGTCT
60.04
CGACGCTGTACCTCATGGAA
59.83
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAGCCGCTTCTCCAAGTCT
60.04
TTCGACGCTGTACCTCATGG
59.83
167
PCR template sequence:
AAGACTTTGAGGCCCGTGGAAGCCGCTTCTCCAAGTCTGCTGATGAGAGACAGCGCATGTTAGTTCAGCGCAAGGATGACCTCCTGCAGCAGGCTCGAAATTATTTGGCAACATCTGGTTATCTATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-32-5p(1), mmu-miR-206-3p(1), mmu-miR-363-3p(1), mmu-miR-153-3p(1), mmu-miR-370-3p(1), mmu-miR-362-5p(1), mmu-miR-325-3p(1), mmu-miR-207(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAGGCTCGAAATTATTTGGCAACA
siRNA sets
AAATAATTTCGAGCCTGCT, CAAATAATTTCGAGCCTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCAMFR_944_ORF_1
0.9279
0.254895517
0.993111718
1038
ORF sequence:
ATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGAATTATTTGCGAGTGGTAGGAAACATGGAAGCCAGGTTTGCTGTTGCAACTCCAGAGGAACTAGCTGTCAATAATGATGACTGTGCAATCTGCTGGGACTCCATGCAGGCTGCAAGGAAACTGCCCTGTGGACATCTTTTTCACAACTCCTGCCTTCGTTCTTGGCTAGAACAAGACACCTCTTGTCCAACATGCAGAATGTCTCTTAATATTGCTGATGGCAGTCGTGCCAGGGAAGACCATCAAGGAGAGAACCTGGACGAGAACTTGGTTCCTGTAGCAGCTGCCGAAGGCAGGCCTCGCTTGAACCAGCACAATCACTTCTTCCACTTCGATGGGTCCCGGATTGCAAGCTGGCTGCCAAGTTTTTCAGTTGAAGTGATGCACACTACCAACATTCTTGGCATCACGCAGGCAAGCAACTCTCAGCTAAATGCCATGGCTCATCAGATTCAGGAGATGTTCCCTCAGGTCCCGTACCACCTTGTGCTCCAGGACCTCCAGATGACACGCTCCGTGGAGATAACAACAGATAACATCTTAGAAGGACGGATTCAAGTACCTTTCCCCACGCAGCGGTCGGATAGCCTGAGGCCTGCACTGAACAGCCCAGTGGAGAGGCCCAGCCCTGACCTGGAGGAGGGAGAAGCTTCTGTCCAGACGGAGCGTGTACCACTGGACCTCAGTCCTCGCCTAGAGGAGACCTTGGACTTCAGTGAGGTAGAACTAGAGCCTATTGAGGTGGAAGACTTTGAGGCCCGTGGAAGCCGCTTCTCCAAGTCTGCTGATGAGAGACAGCGCATGTTAGTTCAGCGCAAGGATGACCTCCTGCAGCAGGCTCGAAATTATTTGGCAACATCTGGTTATCTATGGCTAGCTTGGTCATCTTTATGCAACTTCGTTACCTGTTCCATGAGGTACAGCGTCGAATCCGTCGACACAAGAATTATTTGCGAGTGGTAG
Peptide sequence:
MASLVIFMQLRYLFHEVQRRIRRHKNYLRVVGNMEARFAVATPEELAVNNDDCAICWDSMQAARKLPCGHLFHNSCLRSWLEQDTSCPTCRMSLNIADGSRAREDHQGENLDENLVPVAAAEGRPRLNQHNHFFHFDGSRIASWLPSFSVEVMHTTNILGITQASNSQLNAMAHQIQEMFPQVPYHLVLQDLQMTRSVEITTDNILEGRIQVPFPTQRSDSLRPALNSPVERPSPDLEEGEASVQTERVPLDLSPRLEETLDFSEVELEPIEVEDFEARGSRFSKSADERQRMLVQRKDDLLQQARNYLATSGYLWLAWSSLCNFVTCSMRYSVESVDTRIICEW
IRESfinder result
IRESfinder score
0.42763303
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page