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mmu_circGne_811
Basic information of circular RNA
PanCircBase ID:
mmu_circGne_811
mm39_Chr. Position ID:
chr4|44055204|44066960|-
Gene name:
Gne
Transcript:
ENSMUST00000030201.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,4571,11550
Genomic length:
11756
Exon/intron sizes in nt:
153,452,206
Flanking exon/introns:
chr4:44052983-44055204|chr4:44066960-44084047
Splice length:
811
Other database IDs:
circAtlas: mmu-Gne_0014
circAtlas: hsa-GNE_0009, CIRCpedia: HSA_CIRCpedia_125521
Human Ortholog IDs:
Mature spliced Sequence:
GAACTCTATTTTAAGAAACTCTCAAGTAAAAAGAAGCAAGTCATGGAGAAGAACGGGAACAACCGAAAGCTCCGGGTTTGCGTTGCCACCTGCAACCGAGCTGACTACTCCAAACTGGCCCCGATCATGTTCGGCATCAAGACAGAGCCCGCGTTCTTTGAGTTGGACGTGGTGGTGCTCGGCTCCCACCTGATTGACGACTATGGAAACACATACCGCATGATTGAGCAAGATGACTTTGACATTAACACCAGGCTCCACACGATTGTTAGAGGGGAAGATGAAGCGGCCATGGTAGAGTCGGTAGGCCTAGCGCTCGTGAAGCTACCGGACGTCCTCAATCGCCTGAAGCCCGACATCATGATTGTTCACGGAGACCGATTTGACGCCCTTGCTCTGGCTACGTCTGCTGCCTTGATGAACATCCGCATCCTTCACATTGAAGGAGGCGAGGTCAGCGGGACCATTGATGACTCTATCAGACACGCCATAACAAAACTGGCTCACTACCATGTGTGCTGCACTAGAAGTGCAGAGCAGCACCTGATCTCTATGTGCGAGGACCACGACCGCATCCTGTTGGCAGGCTGCCCTTCCTATGACAAACTGCTCTCCGCCAAGAACAAAGACTATATGAGCATCATTCGGATGTGGCTAGGCGATGATGTAAAATGTAAGGATTACATCGTTGCCCTGCAGCATCCCGTGACCACTGACATTAAGCATTCCATAAAGATGTTTGAGCTAACACTGGATGCCCTGATCTCGTTTAACAAGAGGACCCTAGTTCTGTTTCCAAATATCGATGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACTGGATGCCCTGATCTCG
60.25
AAACCCGGAGCTTTCGGTT
59.85
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTAACACTGGATGCCCTGA
59.75
AAACCCGGAGCTTTCGGTT
59.85
147
PCR template sequence:
ACTGACATTAAGCATTCCATAAAGATGTTTGAGCTAACACTGGATGCCCTGATCTCGTTTAACAAGAGGACCCTAGTTCTGTTTCCAAATATCGATGCAGGAACTCTATTTTAAGAAACTCTCAAGTAAAAAGAAGCAAGTCATGGAGAAGAACGGGAACAACCGAAAGCTCCGGGTTTGCGTTGCCACCTGCAACCGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-199a-5p(1), mmu-miR-15b-5p(1), mmu-miR-214-3p(1), mmu-miR-433-3p(1), mmu-miR-207(1), mmu-miR-544-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATATCGATGCAGGAACTCTATTTTA
siRNA sets
AAAATAGAGTTCCTGCATC, AATAGAGTTCCTGCATCGA, ATAGAGTTCCTGCATCGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGNE_811_ORF_1
1.3144
0.423346095
0.991696251
816
ORF sequence:
ATGCAGGAACTCTATTTTAAGAAACTCTCAAGTAAAAAGAAGCAAGTCATGGAGAAGAACGGGAACAACCGAAAGCTCCGGGTTTGCGTTGCCACCTGCAACCGAGCTGACTACTCCAAACTGGCCCCGATCATGTTCGGCATCAAGACAGAGCCCGCGTTCTTTGAGTTGGACGTGGTGGTGCTCGGCTCCCACCTGATTGACGACTATGGAAACACATACCGCATGATTGAGCAAGATGACTTTGACATTAACACCAGGCTCCACACGATTGTTAGAGGGGAAGATGAAGCGGCCATGGTAGAGTCGGTAGGCCTAGCGCTCGTGAAGCTACCGGACGTCCTCAATCGCCTGAAGCCCGACATCATGATTGTTCACGGAGACCGATTTGACGCCCTTGCTCTGGCTACGTCTGCTGCCTTGATGAACATCCGCATCCTTCACATTGAAGGAGGCGAGGTCAGCGGGACCATTGATGACTCTATCAGACACGCCATAACAAAACTGGCTCACTACCATGTGTGCTGCACTAGAAGTGCAGAGCAGCACCTGATCTCTATGTGCGAGGACCACGACCGCATCCTGTTGGCAGGCTGCCCTTCCTATGACAAACTGCTCTCCGCCAAGAACAAAGACTATATGAGCATCATTCGGATGTGGCTAGGCGATGATGTAAAATGTAAGGATTACATCGTTGCCCTGCAGCATCCCGTGACCACTGACATTAAGCATTCCATAAAGATGTTTGAGCTAACACTGGATGCCCTGATCTCGTTTAACAAGAGGACCCTAGTTCTGTTTCCAAATATCGATGCA
Peptide sequence:
MQELYFKKLSSKKKQVMEKNGNNRKLRVCVATCNRADYSKLAPIMFGIKTEPAFFELDVVVLGSHLIDDYGNTYRMIEQDDFDINTRLHTIVRGEDEAAMVESVGLALVKLPDVLNRLKPDIMIVHGDRFDALALATSAALMNIRILHIEGGEVSGTIDDSIRHAITKLAHYHVCCTRSAEQHLISMCEDHDRILLAGCPSYDKLLSAKNKDYMSIIRMWLGDDVKCKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDA
IRESfinder result
IRESfinder score
0.425754079
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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