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mmu_circGne_1024
Basic information of circular RNA
PanCircBase ID:
mmu_circGne_1024
mm39_Chr. Position ID:
chr4|44052770|44066960|-
Gene name:
Gne
Transcript:
ENSMUST00000030201.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,4,3,2
Exon/intron offsets:
0,2434,7005,13984
Genomic length:
14190
Exon/intron sizes in nt:
2,13,15,34,52,206
Flanking exon/introns:
chr4:44045990-44052770|chr4:44066960-44084047
Splice length:
1024
Other database IDs:
circAtlas: mmu-Gne_0005
circBase: hsa_circ_0138729, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_64058
Human Ortholog IDs:
Mature spliced Sequence:
GAACTCTATTTTAAGAAACTCTCAAGTAAAAAGAAGCAAGTCATGGAGAAGAACGGGAACAACCGAAAGCTCCGGGTTTGCGTTGCCACCTGCAACCGAGCTGACTACTCCAAACTGGCCCCGATCATGTTCGGCATCAAGACAGAGCCCGCGTTCTTTGAGTTGGACGTGGTGGTGCTCGGCTCCCACCTGATTGACGACTATGGAAACACATACCGCATGATTGAGCAAGATGACTTTGACATTAACACCAGGCTCCACACGATTGTTAGAGGGGAAGATGAAGCGGCCATGGTAGAGTCGGTAGGCCTAGCGCTCGTGAAGCTACCGGACGTCCTCAATCGCCTGAAGCCCGACATCATGATTGTTCACGGAGACCGATTTGACGCCCTTGCTCTGGCTACGTCTGCTGCCTTGATGAACATCCGCATCCTTCACATTGAAGGAGGCGAGGTCAGCGGGACCATTGATGACTCTATCAGACACGCCATAACAAAACTGGCTCACTACCATGTGTGCTGCACTAGAAGTGCAGAGCAGCACCTGATCTCTATGTGCGAGGACCACGACCGCATCCTGTTGGCAGGCTGCCCTTCCTATGACAAACTGCTCTCCGCCAAGAACAAAGACTATATGAGCATCATTCGGATGTGGCTAGGCGATGATGTAAAATGTAAGGATTACATCGTTGCCCTGCAGCATCCCGTGACCACTGACATTAAGCATTCCATAAAGATGTTTGAGCTAACACTGGATGCCCTGATCTCGTTTAACAAGAGGACCCTAGTTCTGTTTCCAAATATCGATGCAGGCAGCAAGGAGATGGTTCGAGTGATGCGGAAGAAGGGCATCGAGCATCACCCCAATTTCCGTGCAGTCAAGCACGTCCCGTTTGACCAGTTCATACAGCTGGTCGCCCACGCTGGCTGCATGATTGGGAATAGCAGCTGCGGCGTGCGAGAGGTTGGCGCTTTCGGAACACCCGTGATCAACCTGGGCACAAGGCAGATAGGAAGAGAAACCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTGCATGATTGGGAATAGC
59.73
CGGTTGTTCCCGTTCTTCTC
58.85
165
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCTGCATGATTGGGAATAGC
59.73
AAACCCGGAGCTTTCGGTT
59.85
179
PCR template sequence:
GGCTGCATGATTGGGAATAGCAGCTGCGGCGTGCGAGAGGTTGGCGCTTTCGGAACACCCGTGATCAACCTGGGCACAAGGCAGATAGGAAGAGAAACCGGAACTCTATTTTAAGAAACTCTCAAGTAAAAAGAAGCAAGTCATGGAGAAGAACGGGAACAACCGAAAGCTCCGGGTTTGCGTTGCCACCTGCAACCGAG
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
GGAAGAGAAACCGGAACTCTATTTTA
siRNA sets
AAATAGAGTTCCGGTTTCT, AAAATAGAGTTCCGGTTTC, TAAAATAGAGTTCCGGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGNE_1024_ORF_1
1.2947
0.415992622
0.997539665
996
ORF sequence:
ATGGAGAAGAACGGGAACAACCGAAAGCTCCGGGTTTGCGTTGCCACCTGCAACCGAGCTGACTACTCCAAACTGGCCCCGATCATGTTCGGCATCAAGACAGAGCCCGCGTTCTTTGAGTTGGACGTGGTGGTGCTCGGCTCCCACCTGATTGACGACTATGGAAACACATACCGCATGATTGAGCAAGATGACTTTGACATTAACACCAGGCTCCACACGATTGTTAGAGGGGAAGATGAAGCGGCCATGGTAGAGTCGGTAGGCCTAGCGCTCGTGAAGCTACCGGACGTCCTCAATCGCCTGAAGCCCGACATCATGATTGTTCACGGAGACCGATTTGACGCCCTTGCTCTGGCTACGTCTGCTGCCTTGATGAACATCCGCATCCTTCACATTGAAGGAGGCGAGGTCAGCGGGACCATTGATGACTCTATCAGACACGCCATAACAAAACTGGCTCACTACCATGTGTGCTGCACTAGAAGTGCAGAGCAGCACCTGATCTCTATGTGCGAGGACCACGACCGCATCCTGTTGGCAGGCTGCCCTTCCTATGACAAACTGCTCTCCGCCAAGAACAAAGACTATATGAGCATCATTCGGATGTGGCTAGGCGATGATGTAAAATGTAAGGATTACATCGTTGCCCTGCAGCATCCCGTGACCACTGACATTAAGCATTCCATAAAGATGTTTGAGCTAACACTGGATGCCCTGATCTCGTTTAACAAGAGGACCCTAGTTCTGTTTCCAAATATCGATGCAGGCAGCAAGGAGATGGTTCGAGTGATGCGGAAGAAGGGCATCGAGCATCACCCCAATTTCCGTGCAGTCAAGCACGTCCCGTTTGACCAGTTCATACAGCTGGTCGCCCACGCTGGCTGCATGATTGGGAATAGCAGCTGCGGCGTGCGAGAGGTTGGCGCTTTCGGAACACCCGTGATCAACCTGGGCACAAGGCAGATAGGAAGAGAAACCGGAACTCTATTTTAA
Peptide sequence:
MEKNGNNRKLRVCVATCNRADYSKLAPIMFGIKTEPAFFELDVVVLGSHLIDDYGNTYRMIEQDDFDINTRLHTIVRGEDEAAMVESVGLALVKLPDVLNRLKPDIMIVHGDRFDALALATSAALMNIRILHIEGGEVSGTIDDSIRHAITKLAHYHVCCTRSAEQHLISMCEDHDRILLAGCPSYDKLLSAKNKDYMSIIRMWLGDDVKCKDYIVALQHPVTTDIKHSIKMFELTLDALISFNKRTLVLFPNIDAGSKEMVRVMRKKGIEHHPNFRAVKHVPFDQFIQLVAHAGCMIGNSSCGVREVGAFGTPVINLGTRQIGRETGTLF
IRESfinder result
IRESfinder score
0.379131571
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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