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mmu_circPfas_1371
Basic information of circular RNA
PanCircBase ID:
mmu_circPfas_1371
mm39_Chr. Position ID:
chr11|68888489|68894698|-
Gene name:
Pfas
Transcript:
ENSMUST00000021282.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,249,2345,2581,2785,3210,3443,4069,4816,6032
Genomic length:
6209
Exon/intron sizes in nt:
1,29,13,21,29,12,51,41,00,00,00,00,00,00,000
Flanking exon/introns:
chr11:68885157-68888489|chr11:68894698-68899228
Splice length:
1371
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_22994
Human Ortholog IDs:
Mature spliced Sequence:
GAGCCAAATTCTTTTCTAAAAGGTCATCTGCAGAAATGGCCCCTGTCCTTCACTTTTATGTCCGCCCCTCTGGCCATGAGGGGGCAGCATCTGGACGTGTTTTTCGGAGACTACAAGAGAAACTGCCAACACTTCAGAGTGTGGAGACTGAGCTGTGCTACAATGTACACTGGGCAGCTGAGACCCTTCCATGGGCTGAGGAGATGAAGAAGTTGATGTGGCTGTTCGGCTGCCCTTTGGTGCGGGATGATGTTGCTCAGGAGCCCTGGCTTGTTCCTGGCTCCAACGATTTGTTGCTGGAGGTGGGACCCAGGCTGAATTTCTCGACTCCAGCATCGACCAACATTGTTTCTGTGTGCCAGGCAGCCGGGCTGAGGGCTGTGGATCGGGTAGAGACCACCCGACGTTACCGACTTTCGTTTACCGACCACCCTACAGCTGAAATGGAAGCCATCTCTCTGGCCGCCTTGCACGACCGGATGACAGAGCAGCACTACCCTGACCCCATCCAGAGCTTCTCTCCTCAGAGCATTCCAGCCCCACTCAAGGGCTCCATCGACATACTAGCTGAGGGTCGGCCTGCCCTGGAGAAGGCCAACCAGGAGCTAGGTTTGGCTCTTGACTCCTGGGACCTCGATTTCTATACCAAGCGCTTTCAAGAGCTGCAGCGGAACCCCAGTACAGTGGAGGTCTTTGACTTGGCTCAGTCCAATAGTGAGCACAGCCGACATTGGTTCTTCAAGGGCCAGCTCCATGTGGATGGGAAGAAGCTAGCGCATTCCCTCTTTGAATCCATCATGAGCACTCAGGCATCCTCCAACCCTAACAATGTCCTCAAGTTCTGTGACAACAGCAGTGCAATCCAGGGGAAGAAAGTCAAATTCCTGCGGCCGGAGGACTCTACCCGCCCAAGCTGCTTCCAGCAACAGCAGGGGCTTAGACATGTTGTCTTCACAGCAGAGACACATAACTTCCCCACAGGAGTGGCCCCCTTCAGCGGTGCAACCACAGGCACGGGTGGCCGCATCAGAGACGTCCAGTGCACAGGCCGTGGGGCCCACGTGGTAGCTGGCACTGCTGGCTATTGCTTTGGAAACCTGCACATCCCAGATTATAATCTGCCCTGGGAGGACCCAAGCTTCCAGTATCCTGGGAACTTTGCCAGGCCTTTGGAGGTTGCTATTGAGGCCAGCAATGGAGCATCTGACTATGGCAACAAGTTTGGAGAGCCAGTGCTGGCTGGATTTGCCCGCTCTTTGGGTCTCCAGCTTCCAGATGGTCAGAGACGTGAGTGGATCAAGCCCATCATGTTCAGTGGCGGCATTGGGTCCATGGAAGCCAAACATGTAGGCAAAAAGCCCCCAGAGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGAGTGGATCAAGCCCAT
60.11
AAAAGTGAAGGACAGGGGCC
60.18
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGAGTGGATCAAGCCCAT
60.11
CCAGAGGGGCGGACATAAAA
59.75
158
PCR template sequence:
CCAGATGGTCAGAGACGTGAGTGGATCAAGCCCATCATGTTCAGTGGCGGCATTGGGTCCATGGAAGCCAAACATGTAGGCAAAAAGCCCCCAGAGCCAGGAGCCAAATTCTTTTCTAAAAGGTCATCTGCAGAAATGGCCCCTGTCCTTCACTTTTATGTCCGCCCCTCTGGCCATGAGGGGGCAGCATCTGGACGTGT
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-199a-5p(1), mmu-miR-135a-5p(1), mmu-miR-326-3p(1), mmu-miR-433-3p(1), mmu-miR-370-3p(1), mmu-miR-539-5p(1), mmu-miR-3065-5p(1), mmu-miR-3470b(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCCCAGAGCCAGGAGCCAAATTCTT
siRNA sets
AATTTGGCTCCTGGCTCTG, AGAATTTGGCTCCTGGCTC, ATTTGGCTCCTGGCTCTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPFAS_1371_ORF_1
0.9047
0.308718074
0.999999965
2706
ORF sequence:
ATGGCCCCTGTCCTTCACTTTTATGTCCGCCCCTCTGGCCATGAGGGGGCAGCATCTGGACGTGTTTTTCGGAGACTACAAGAGAAACTGCCAACACTTCAGAGTGTGGAGACTGAGCTGTGCTACAATGTACACTGGGCAGCTGAGACCCTTCCATGGGCTGAGGAGATGAAGAAGTTGATGTGGCTGTTCGGCTGCCCTTTGGTGCGGGATGATGTTGCTCAGGAGCCCTGGCTTGTTCCTGGCTCCAACGATTTGTTGCTGGAGGTGGGACCCAGGCTGAATTTCTCGACTCCAGCATCGACCAACATTGTTTCTGTGTGCCAGGCAGCCGGGCTGAGGGCTGTGGATCGGGTAGAGACCACCCGACGTTACCGACTTTCGTTTACCGACCACCCTACAGCTGAAATGGAAGCCATCTCTCTGGCCGCCTTGCACGACCGGATGACAGAGCAGCACTACCCTGACCCCATCCAGAGCTTCTCTCCTCAGAGCATTCCAGCCCCACTCAAGGGCTCCATCGACATACTAGCTGAGGGTCGGCCTGCCCTGGAGAAGGCCAACCAGGAGCTAGGTTTGGCTCTTGACTCCTGGGACCTCGATTTCTATACCAAGCGCTTTCAAGAGCTGCAGCGGAACCCCAGTACAGTGGAGGTCTTTGACTTGGCTCAGTCCAATAGTGAGCACAGCCGACATTGGTTCTTCAAGGGCCAGCTCCATGTGGATGGGAAGAAGCTAGCGCATTCCCTCTTTGAATCCATCATGAGCACTCAGGCATCCTCCAACCCTAACAATGTCCTCAAGTTCTGTGACAACAGCAGTGCAATCCAGGGGAAGAAAGTCAAATTCCTGCGGCCGGAGGACTCTACCCGCCCAAGCTGCTTCCAGCAACAGCAGGGGCTTAGACATGTTGTCTTCACAGCAGAGACACATAACTTCCCCACAGGAGTGGCCCCCTTCAGCGGTGCAACCACAGGCACGGGTGGCCGCATCAGAGACGTCCAGTGCACAGGCCGTGGGGCCCACGTGGTAGCTGGCACTGCTGGCTATTGCTTTGGAAACCTGCACATCCCAGATTATAATCTGCCCTGGGAGGACCCAAGCTTCCAGTATCCTGGGAACTTTGCCAGGCCTTTGGAGGTTGCTATTGAGGCCAGCAATGGAGCATCTGACTATGGCAACAAGTTTGGAGAGCCAGTGCTGGCTGGATTTGCCCGCTCTTTGGGTCTCCAGCTTCCAGATGGTCAGAGACGTGAGTGGATCAAGCCCATCATGTTCAGTGGCGGCATTGGGTCCATGGAAGCCAAACATGTAGGCAAAAAGCCCCCAGAGCCAGGAGCCAAATTCTTTTCTAAAAGGTCATCTGCAGAAATGGCCCCTGTCCTTCACTTTTATGTCCGCCCCTCTGGCCATGAGGGGGCAGCATCTGGACGTGTTTTTCGGAGACTACAAGAGAAACTGCCAACACTTCAGAGTGTGGAGACTGAGCTGTGCTACAATGTACACTGGGCAGCTGAGACCCTTCCATGGGCTGAGGAGATGAAGAAGTTGATGTGGCTGTTCGGCTGCCCTTTGGTGCGGGATGATGTTGCTCAGGAGCCCTGGCTTGTTCCTGGCTCCAACGATTTGTTGCTGGAGGTGGGACCCAGGCTGAATTTCTCGACTCCAGCATCGACCAACATTGTTTCTGTGTGCCAGGCAGCCGGGCTGAGGGCTGTGGATCGGGTAGAGACCACCCGACGTTACCGACTTTCGTTTACCGACCACCCTACAGCTGAAATGGAAGCCATCTCTCTGGCCGCCTTGCACGACCGGATGACAGAGCAGCACTACCCTGACCCCATCCAGAGCTTCTCTCCTCAGAGCATTCCAGCCCCACTCAAGGGCTCCATCGACATACTAGCTGAGGGTCGGCCTGCCCTGGAGAAGGCCAACCAGGAGCTAGGTTTGGCTCTTGACTCCTGGGACCTCGATTTCTATACCAAGCGCTTTCAAGAGCTGCAGCGGAACCCCAGTACAGTGGAGGTCTTTGACTTGGCTCAGTCCAATAGTGAGCACAGCCGACATTGGTTCTTCAAGGGCCAGCTCCATGTGGATGGGAAGAAGCTAGCGCATTCCCTCTTTGAATCCATCATGAGCACTCAGGCATCCTCCAACCCTAACAATGTCCTCAAGTTCTGTGACAACAGCAGTGCAATCCAGGGGAAGAAAGTCAAATTCCTGCGGCCGGAGGACTCTACCCGCCCAAGCTGCTTCCAGCAACAGCAGGGGCTTAGACATGTTGTCTTCACAGCAGAGACACATAACTTCCCCACAGGAGTGGCCCCCTTCAGCGGTGCAACCACAGGCACGGGTGGCCGCATCAGAGACGTCCAGTGCACAGGCCGTGGGGCCCACGTGGTAGCTGGCACTGCTGGCTATTGCTTTGGAAACCTGCACATCCCAGATTATAATCTGCCCTGGGAGGACCCAAGCTTCCAGTATCCTGGGAACTTTGCCAGGCCTTTGGAGGTTGCTATTGAGGCCAGCAATGGAGCATCTGACTATGGCAACAAGTTTGGAGAGCCAGTGCTGGCTGGATTTGCCCGCTCTTTGGGTCTCCAGCTTCCAGATGGTCAGAGACGTGAGTGGATCAAGCCCATCATGTTCAGTGGCGGCATTGGGTCCATGGAAGCCAAACATGTAGGCAAAAAGCCCCCAGAGCCA
Peptide sequence:
MAPVLHFYVRPSGHEGAASGRVFRRLQEKLPTLQSVETELCYNVHWAAETLPWAEEMKKLMWLFGCPLVRDDVAQEPWLVPGSNDLLLEVGPRLNFSTPASTNIVSVCQAAGLRAVDRVETTRRYRLSFTDHPTAEMEAISLAALHDRMTEQHYPDPIQSFSPQSIPAPLKGSIDILAEGRPALEKANQELGLALDSWDLDFYTKRFQELQRNPSTVEVFDLAQSNSEHSRHWFFKGQLHVDGKKLAHSLFESIMSTQASSNPNNVLKFCDNSSAIQGKKVKFLRPEDSTRPSCFQQQQGLRHVVFTAETHNFPTGVAPFSGATTGTGGRIRDVQCTGRGAHVVAGTAGYCFGNLHIPDYNLPWEDPSFQYPGNFARPLEVAIEASNGASDYGNKFGEPVLAGFARSLGLQLPDGQRREWIKPIMFSGGIGSMEAKHVGKKPPEPGAKFFSKRSSAEMAPVLHFYVRPSGHEGAASGRVFRRLQEKLPTLQSVETELCYNVHWAAETLPWAEEMKKLMWLFGCPLVRDDVAQEPWLVPGSNDLLLEVGPRLNFSTPASTNIVSVCQAAGLRAVDRVETTRRYRLSFTDHPTAEMEAISLAALHDRMTEQHYPDPIQSFSPQSIPAPLKGSIDILAEGRPALEKANQELGLALDSWDLDFYTKRFQELQRNPSTVEVFDLAQSNSEHSRHWFFKGQLHVDGKKLAHSLFESIMSTQASSNPNNVLKFCDNSSAIQGKKVKFLRPEDSTRPSCFQQQQGLRHVVFTAETHNFPTGVAPFSGATTGTGGRIRDVQCTGRGAHVVAGTAGYCFGNLHIPDYNLPWEDPSFQYPGNFARPLEVAIEASNGASDYGNKFGEPVLAGFARSLGLQLPDGQRREWIKPIMFSGGIGSMEAKHVGKKPPEP
IRESfinder result
IRESfinder score
0.49656301
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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