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mmu_circNbas_1960
Basic information of circular RNA
PanCircBase ID:
mmu_circNbas_1960
mm39_Chr. Position ID:
chr12|13335183|13386411|+
Gene name:
Nbas
Transcript:
ENSMUST00000042953.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
7,8,9,10,11,12,13,14,15,16,17,18,19,20,21
Exon/intron offsets:
0,3488,4699,14910,21721,24993,32515,36462,37673,39086,43153,45434,45841,50648,51091
Genomic length:
51228
Exon/intron sizes in nt:
134,134,99,139,69,129,64,194,258,126,152,141,79,105,137
Flanking exon/introns:
chr12:13329432-13335183|chr12:13386411-13402783
Splice length:
1960
Other database IDs:
circBase: mmu_circ_0003811, CIRCpedia: MMU_CIRCpedia_7886, circAtlas: mmu-Nbas_0028
circBase: hsa_circ_0052769, circAtlas: hsa-NBAS_0046, CIRCpedia: HSA_CIRCpedia_38229
Human Ortholog IDs:
Mature spliced Sequence:
TTCCAAAAGACCCAAAGCCCCAGTGGAGACGGGTAGCATGGAGTTACGACTGCACACTGCTGGCCTATGCCGAGAGCACAGGGACTGTAAGGGTGTTTGATCTTATGGGCAGCGAGCTCTTTGTCATTGCCCCGGCATCTGTCTTTGCTGGGGACTTAAGCTACGCCATTGCTGGGTTGGTATTTTTAGAATACAAAGCCAGTGCACAGTGGTCTGCAGAGCTCTTGGTCATCAATTACCGGGGAGAACTTAGAAGTTACCTTGTCAGTGTTGGAACAAATCAGAGCTACCAAGAGAGTCACAGTTTCAGCTTTAGTGGTCATTATCCGCATGGAATAAATACTGCTATTTACCACCCTGGTCATAGGCTTTTACTGGTTGGTGGATGTGAAACTGCTGAACTGGGCATTTCCAAAGCTGCTAGCTGTGGCCTTTCTGCATGGAGAGTCCTTTCAGGCTCACCGTATTATAAGCAAGTTACTAATGGTGGAGACAGGGTCACTGAGGTGCCAAAGACCCTGGGATTATTAAAGCTGCTAAGTGTCAAGCTTTCCCCTCGCCTGGGACAAGAACAGGATGGGATCTTCAAGATGGGCCTGTCTCCTGACGGGAGCCTCCTTGCGGCGATTCACTTCTCAGGGAAGCTGAGCATCTGGGCCATTCCATCTCTGAAGCAACAAGGAGTCTGGCGTCAAGATGAGCAGCCAGGCTACAATGAGCTTAATCCTGATTGGAGGTTGTCTCCTGAGAAGAGAAAGAAAGTAAAAGATAAAGAGTCCTTTTATCCATTGATTGATGTCAATTGGTGGGCAGACGGCGCAGTGACCCTGGCTCGCTGCTCCGGTGCATTAACTGTTTCATCAGCGAAAAGTTTGAAGAATTTACTGGGAAAATCCTGCGAATGGTTTGAGCCCTCTCCCCAGGTCACTGCCACCCATGATGGGGGGTTCTTAAGTTTGGAGTGTGAAATTAAACTTGCCCCTAAAAGATCTCGAGTGGAGATGAGGGCTGGAGAAGAAGATGAAGGGGAAGTGGATTCTGACTCAGATCCTGAGACCTCTGCCAAGGCTCGCTATTTTGGGTACATCAAGCAAGGCCTTTACTTAGTTACGGAGATGGAGAGGTTTGCACCTCCTCGGAAACGGCCTCGAACTATCACAAAGAACTACCGCCTTGTGAGTCTGCGCTCCACAACTCCAGAGGAGCTTTATCAGAGAAAGATTGACAGTGAAGACTATGAAGAAGCCTTGTGTTTGGCTCACACCTACGGCCTGGATACTGACCTTGTCTATCAGAGGCAGTGGAGGAAGTCCGCTGTCAACAGTGCTTCAATTCACAATTACTTGAGTAAAATCAAGAAGCGGTCTTGGGTTCTCCATGAGTGTTTGGAGAGAGTTCCTGAGAACGTGGACGCTGCCAAGGAACTGCTGCAGTATGGCTTGAAAGGCACAGACCTGGAGGCTCTCGTCGCCATAGGAAAGGGTGTGGATGATGGCAGATTTACCTTACCAGGTGACATAGACATTGACAGCATTGCCTATGAGGAGCTTTCCCCAGCAGACAAAGAGCCTTCCAAGAGCAAACGGCAGGAAGAGCTTAAGAAGAGACGCGATCTGCTTAAATTAGTGAACTTTTCAAAGTTGACCCTGGAACAAAAGGAACTGTGCCGTTGTAGACTGAAGTTATTAACCTTCTTAGATCGTCTTGCAACATATGAGGAAATCCTAGGGGCGCCACATGCATCTGAACAGAGGTATGATGCTGAATTTTTTAAGAAGTTCAGAAGTCAGAATATTGTTCTCTCAGCAAGAACGTATGCTCGGGAGAGTAATGTCCAAGCCCTGGAAATCCTGCTGACATACCACGGCTCTCATCTGCTCCCTCATCGCCTTGCCATCCTCTCTAACTTCCCAGAAACCACCTCTCCACACGAATATGCTGTTTTGTTGCCAGAGGCTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGAAACCACCTCTCCAC
59.96
CCCTTACAGTCCCTGTGCTC
59.75
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCCAGAAACCACCTCTCCA
60.1
CCCTTACAGTCCCTGTGCTC
59.75
145
PCR template sequence:
ACCACGGCTCTCATCTGCTCCCTCATCGCCTTGCCATCCTCTCTAACTTCCCAGAAACCACCTCTCCACACGAATATGCTGTTTTGTTGCCAGAGGCTTGTTCCAAAAGACCCAAAGCCCCAGTGGAGACGGGTAGCATGGAGTTACGACTGCACACTGCTGGCCTATGCCGAGAGCACAGGGACTGTAAGGGTGTTTGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-34a-5p(1), mmu-miR-19b-3p(1), mmu-miR-26a-5p(1), mmu-miR-205-5p(1), mmu-miR-19a-3p(1), mmu-miR-320-3p(1), mmu-miR-339-5p(1), mmu-miR-503-5p(1), mmu-miR-433-5p(1), mmu-miR-351-5p(1), mmu-miR-26b-5p(1), mmu-miR-501-3p(1), mmu-miR-324-3p(1), mmu-miR-384-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-3065-5p(1), mmu-miR-323-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGCCAGAGGCTTGTTCCAAAAGACCC
siRNA sets
TTTGGAACAAGCCTCTGGC, GGGTCTTTTGGAACAAGCC, TTTTGGAACAAGCCTCTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNBAS_1960_ORF_1
0.8205
0.170320848
0.999986291
1983
ORF sequence:
ATGCTGTTTTGTTGCCAGAGGCTTGTTCCAAAAGACCCAAAGCCCCAGTGGAGACGGGTAGCATGGAGTTACGACTGCACACTGCTGGCCTATGCCGAGAGCACAGGGACTGTAAGGGTGTTTGATCTTATGGGCAGCGAGCTCTTTGTCATTGCCCCGGCATCTGTCTTTGCTGGGGACTTAAGCTACGCCATTGCTGGGTTGGTATTTTTAGAATACAAAGCCAGTGCACAGTGGTCTGCAGAGCTCTTGGTCATCAATTACCGGGGAGAACTTAGAAGTTACCTTGTCAGTGTTGGAACAAATCAGAGCTACCAAGAGAGTCACAGTTTCAGCTTTAGTGGTCATTATCCGCATGGAATAAATACTGCTATTTACCACCCTGGTCATAGGCTTTTACTGGTTGGTGGATGTGAAACTGCTGAACTGGGCATTTCCAAAGCTGCTAGCTGTGGCCTTTCTGCATGGAGAGTCCTTTCAGGCTCACCGTATTATAAGCAAGTTACTAATGGTGGAGACAGGGTCACTGAGGTGCCAAAGACCCTGGGATTATTAAAGCTGCTAAGTGTCAAGCTTTCCCCTCGCCTGGGACAAGAACAGGATGGGATCTTCAAGATGGGCCTGTCTCCTGACGGGAGCCTCCTTGCGGCGATTCACTTCTCAGGGAAGCTGAGCATCTGGGCCATTCCATCTCTGAAGCAACAAGGAGTCTGGCGTCAAGATGAGCAGCCAGGCTACAATGAGCTTAATCCTGATTGGAGGTTGTCTCCTGAGAAGAGAAAGAAAGTAAAAGATAAAGAGTCCTTTTATCCATTGATTGATGTCAATTGGTGGGCAGACGGCGCAGTGACCCTGGCTCGCTGCTCCGGTGCATTAACTGTTTCATCAGCGAAAAGTTTGAAGAATTTACTGGGAAAATCCTGCGAATGGTTTGAGCCCTCTCCCCAGGTCACTGCCACCCATGATGGGGGGTTCTTAAGTTTGGAGTGTGAAATTAAACTTGCCCCTAAAAGATCTCGAGTGGAGATGAGGGCTGGAGAAGAAGATGAAGGGGAAGTGGATTCTGACTCAGATCCTGAGACCTCTGCCAAGGCTCGCTATTTTGGGTACATCAAGCAAGGCCTTTACTTAGTTACGGAGATGGAGAGGTTTGCACCTCCTCGGAAACGGCCTCGAACTATCACAAAGAACTACCGCCTTGTGAGTCTGCGCTCCACAACTCCAGAGGAGCTTTATCAGAGAAAGATTGACAGTGAAGACTATGAAGAAGCCTTGTGTTTGGCTCACACCTACGGCCTGGATACTGACCTTGTCTATCAGAGGCAGTGGAGGAAGTCCGCTGTCAACAGTGCTTCAATTCACAATTACTTGAGTAAAATCAAGAAGCGGTCTTGGGTTCTCCATGAGTGTTTGGAGAGAGTTCCTGAGAACGTGGACGCTGCCAAGGAACTGCTGCAGTATGGCTTGAAAGGCACAGACCTGGAGGCTCTCGTCGCCATAGGAAAGGGTGTGGATGATGGCAGATTTACCTTACCAGGTGACATAGACATTGACAGCATTGCCTATGAGGAGCTTTCCCCAGCAGACAAAGAGCCTTCCAAGAGCAAACGGCAGGAAGAGCTTAAGAAGAGACGCGATCTGCTTAAATTAGTGAACTTTTCAAAGTTGACCCTGGAACAAAAGGAACTGTGCCGTTGTAGACTGAAGTTATTAACCTTCTTAGATCGTCTTGCAACATATGAGGAAATCCTAGGGGCGCCACATGCATCTGAACAGAGGTATGATGCTGAATTTTTTAAGAAGTTCAGAAGTCAGAATATTGTTCTCTCAGCAAGAACGTATGCTCGGGAGAGTAATGTCCAAGCCCTGGAAATCCTGCTGACATACCACGGCTCTCATCTGCTCCCTCATCGCCTTGCCATCCTCTCTAACTTCCCAGAAACCACCTCTCCACACGAATATGCTGTTTTGTTGCCAGAGGCT
Peptide sequence:
MLFCCQRLVPKDPKPQWRRVAWSYDCTLLAYAESTGTVRVFDLMGSELFVIAPASVFAGDLSYAIAGLVFLEYKASAQWSAELLVINYRGELRSYLVSVGTNQSYQESHSFSFSGHYPHGINTAIYHPGHRLLLVGGCETAELGISKAASCGLSAWRVLSGSPYYKQVTNGGDRVTEVPKTLGLLKLLSVKLSPRLGQEQDGIFKMGLSPDGSLLAAIHFSGKLSIWAIPSLKQQGVWRQDEQPGYNELNPDWRLSPEKRKKVKDKESFYPLIDVNWWADGAVTLARCSGALTVSSAKSLKNLLGKSCEWFEPSPQVTATHDGGFLSLECEIKLAPKRSRVEMRAGEEDEGEVDSDSDPETSAKARYFGYIKQGLYLVTEMERFAPPRKRPRTITKNYRLVSLRSTTPEELYQRKIDSEDYEEALCLAHTYGLDTDLVYQRQWRKSAVNSASIHNYLSKIKKRSWVLHECLERVPENVDAAKELLQYGLKGTDLEALVAIGKGVDDGRFTLPGDIDIDSIAYEELSPADKEPSKSKRQEELKKRRDLLKLVNFSKLTLEQKELCRCRLKLLTFLDRLATYEEILGAPHASEQRYDAEFFKKFRSQNIVLSARTYARESNVQALEILLTYHGSHLLPHRLAILSNFPETTSPHEYAVLLPEA
IRESfinder result
IRESfinder score
0.603918396
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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