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mmu_circNt5c2_288
Basic information of circular RNA
PanCircBase ID:
mmu_circNt5c2_288
mm39_Chr. Position ID:
chr19|46892316|46912774|-
Gene name:
Nt5c2
Transcript:
ENSMUST00000235234.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,1097,20384
Genomic length:
20458
Exon/intron sizes in nt:
96,118,74
Flanking exon/introns:
chr19:46887333-46892316|chr19:46912774-46939284
Splice length:
288
Other database IDs:
CIRCpedia: MMU_CIRCpedia_227947, circAtlas: mmu-Nt5c2_0004
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_155882
Human Ortholog IDs:
Mature spliced Sequence:
GGTGTTTGTGAACCGAAGTTTAGCCATGGAAAAAATAAAGTGTTTTGGTTTTGATATGGATTATACCCTAGCCGTGTACAAGTCTCCAGAATATGAATCCCTTGGCTTTGAGCTTACTGTGGAGAGATTAGTTTCCATTGGCTATCCTCAGGAGCTGCTCAGCTTTGCATATGATTCTACATTCCCTACCAGAGGACTTGTCTTTGACACGCTCTATGGAAATCTTTTGAAAGTCGATGCCTATGGAAACCTCTTGGTGTGTGCACATGGATTTAACTTCATAAGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACTTGTCTTTGACACGCT
59.86
GACTTGTACACGGCTAGGGT
59.11
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGACTTGTCTTTGACACGCTC
59.47
GACTTGTACACGGCTAGGGT
59.11
179
PCR template sequence:
CCAGAGGACTTGTCTTTGACACGCTCTATGGAAATCTTTTGAAAGTCGATGCCTATGGAAACCTCTTGGTGTGTGCACATGGATTTAACTTCATAAGAGGGGTGTTTGTGAACCGAAGTTTAGCCATGGAAAAAATAAAGTGTTTTGGTTTTGATATGGATTATACCCTAGCCGTGTACAAGTCTCCAGAATATGAATCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-541-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTTCATAAGAGGGGTGTTTGTGAAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNT5C2_288_ORF_1
0.7415
0.099460522
0.620280357
549
ORF sequence:
ATGGAAAAAATAAAGTGTTTTGGTTTTGATATGGATTATACCCTAGCCGTGTACAAGTCTCCAGAATATGAATCCCTTGGCTTTGAGCTTACTGTGGAGAGATTAGTTTCCATTGGCTATCCTCAGGAGCTGCTCAGCTTTGCATATGATTCTACATTCCCTACCAGAGGACTTGTCTTTGACACGCTCTATGGAAATCTTTTGAAAGTCGATGCCTATGGAAACCTCTTGGTGTGTGCACATGGATTTAACTTCATAAGAGGGGTGTTTGTGAACCGAAGTTTAGCCATGGAAAAAATAAAGTGTTTTGGTTTTGATATGGATTATACCCTAGCCGTGTACAAGTCTCCAGAATATGAATCCCTTGGCTTTGAGCTTACTGTGGAGAGATTAGTTTCCATTGGCTATCCTCAGGAGCTGCTCAGCTTTGCATATGATTCTACATTCCCTACCAGAGGACTTGTCTTTGACACGCTCTATGGAAATCTTTTGAAAGTCGATGCCTATGGAAACCTCTTGGTGTGTGCACATGGATTTAACTTCATAAGA
Peptide sequence:
MEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIRGVFVNRSLAMEKIKCFGFDMDYTLAVYKSPEYESLGFELTVERLVSIGYPQELLSFAYDSTFPTRGLVFDTLYGNLLKVDAYGNLLVCAHGFNFIR
IRESfinder result
IRESfinder score
0.834217682
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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