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mmu_circNsf_351
Basic information of circular RNA
PanCircBase ID:
mmu_circNsf_351
mm39_Chr. Position ID:
chr11|103804141|103807498|-
Gene name:
Nsf
Transcript:
ENSMUST00000103075.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,485,3190
Genomic length:
3357
Exon/intron sizes in nt:
76,108,167
Flanking exon/introns:
chr11:103801424-103804141|chr11:103807498-103816973
Splice length:
351
Other database IDs:
CIRCpedia: MMU_CIRCpedia_1074, circAtlas: mmu-Nsf_0017
Human Ortholog IDs:
Mature spliced Sequence:
TTGCCTTGTATTCGTTTGACAAAGCCAAGCAGTGCATCGGCACAATGACCATCGAGATCGACTTCCTGCAGAAGAAGAACATCGACTCCAACCCTTACGACACCGACAAGATGGCCGCCGAGTTCATCCAGCAGTTCAACAACCAGGCCTTCTCAGTGGGGCAGCAGCTTGTCTTTAGCTTCAATGATAAGCTCTTTGGATTACTGGTGAAGGACATTGAAGCCATGGATCCCAGCATCCTGAAGGGAGAGCCTGCATCAGGCAAAAGGCAGAAGATTGAGGTAGGCCTGGTTGTTGGAAACAGTCAAGTTGCATTTGAAAAAGCAGAAAATTCGTCGCTCAATCTTATCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGTAGGCCTGGTTGTTGGAA
59.89
TCTGCAGGAAGTCGATCTCG
59.26
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTAGGCCTGGTTGTTGGAA
59.89
TTCTGCAGGAAGTCGATCTCG
59.87
144
PCR template sequence:
CCTGCATCAGGCAAAAGGCAGAAGATTGAGGTAGGCCTGGTTGTTGGAAACAGTCAAGTTGCATTTGAAAAAGCAGAAAATTCGTCGCTCAATCTTATCGTTGCCTTGTATTCGTTTGACAAAGCCAAGCAGTGCATCGGCACAATGACCATCGAGATCGACTTCCTGCAGAAGAAGAACATCGACTCCAACCCTTACGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-381-3p(1), mmu-miR-127-5p(1), mmu-miR-484(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCAATCTTATCGTTGCCTTGTATTC
siRNA sets
AATACAAGGCAACGATAAG, AAGGCAACGATAAGATTGA, TACAAGGCAACGATAAGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNSF_351_ORF_1
1.2946
0.543249707
0.983860478
657
ORF sequence:
ATGACCATCGAGATCGACTTCCTGCAGAAGAAGAACATCGACTCCAACCCTTACGACACCGACAAGATGGCCGCCGAGTTCATCCAGCAGTTCAACAACCAGGCCTTCTCAGTGGGGCAGCAGCTTGTCTTTAGCTTCAATGATAAGCTCTTTGGATTACTGGTGAAGGACATTGAAGCCATGGATCCCAGCATCCTGAAGGGAGAGCCTGCATCAGGCAAAAGGCAGAAGATTGAGGTAGGCCTGGTTGTTGGAAACAGTCAAGTTGCATTTGAAAAAGCAGAAAATTCGTCGCTCAATCTTATCGTTGCCTTGTATTCGTTTGACAAAGCCAAGCAGTGCATCGGCACAATGACCATCGAGATCGACTTCCTGCAGAAGAAGAACATCGACTCCAACCCTTACGACACCGACAAGATGGCCGCCGAGTTCATCCAGCAGTTCAACAACCAGGCCTTCTCAGTGGGGCAGCAGCTTGTCTTTAGCTTCAATGATAAGCTCTTTGGATTACTGGTGAAGGACATTGAAGCCATGGATCCCAGCATCCTGAAGGGAGAGCCTGCATCAGGCAAAAGGCAGAAGATTGAGGTAGGCCTGGTTGTTGGAAACAGTCAAGTTGCATTTGAAAAAGCAGAAAATTCGTCGCTCAATCTTATC
Peptide sequence:
MTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLI
IRESfinder result
IRESfinder score
0.552763206
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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