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mmu_circNpat_576
Basic information of circular RNA
PanCircBase ID:
mmu_circNpat_576
mm39_Chr. Position ID:
chr9|53465184|53470507|+
Gene name:
Npat
Transcript:
ENSMUST00000035850.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
7,8,9,10,11,12
Exon/intron offsets:
0,1172,2503,2683,4240,5197
Genomic length:
5323
Exon/intron sizes in nt:
88,85,92,88,97,126
Flanking exon/introns:
chr9:53463774-53465184|chr9:53470507-53473341
Splice length:
576
Other database IDs:
circAtlas: mmu-Npat_0007
Human Ortholog IDs:
Mature spliced Sequence:
ATACAGCTGGAGAGTCTTTGAATATCATTCCTGGTCCTCAGGAAAGGAAAACTCAAACCAGTTTAATGTCTCCTGGTAGACGTAAAAGTGAATCACAAAAGAAGAGTCTCACATCATCTGGACCGCATTCATCAAGGAATTTTCAGGATCCAAATGCATTTGCAGTAGAAAAACAAATGGTTATTGAAAATGCAAGAGAGAAAATATTAAGCAACAAATCTCTTCAAGAAAAACTAGCAGAAAACATAAATAAGTTTTTGACTAGTGATAGTAGTGTTGCTCAAGTACCTAAGCAGACAGACAGCAACCCGACAGAGCCAGAAACGTCAATTGATGAACTGCTAGGCCTTCCGAGTGAAATCCATATGTCTGAAGAAGCCATACAAGATATTTTGGAGCAGACAGAATCAGACCCCGCCTTTCAGGCACTCTTTGATCTTTTTGACTATGGTAAAACAAAGAACAATAAAAATATGCCACAAATCTCTAGTCAACCTATGGAGACTAATTCTAATATAGTCTTGCCTGAAGAAACTAATCTAACAATTAAAAGTTCTTTTGAAACTGAAGAATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTCTAGTCAACCTATGGAGACT
57.28
AGTTTTCCTTTCCTGAGGACCA
59.22
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCACAAATCTCTAGTCAACCTATGG
58.95
AGTTTTCCTTTCCTGAGGACCA
59.22
153
PCR template sequence:
CCACAAATCTCTAGTCAACCTATGGAGACTAATTCTAATATAGTCTTGCCTGAAGAAACTAATCTAACAATTAAAAGTTCTTTTGAAACTGAAGAATCAGATACAGCTGGAGAGTCTTTGAATATCATTCCTGGTCCTCAGGAAAGGAAAACTCAAACCAGTTTAATGTCTCCTGGTAGACGTAAAAGTGAATCACAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGAAGAATCAGATACAGCTGGAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNPAT_576_ORF_1
1.0504
-0.002995035
0.989099982
1086
ORF sequence:
ATGTCTCCTGGTAGACGTAAAAGTGAATCACAAAAGAAGAGTCTCACATCATCTGGACCGCATTCATCAAGGAATTTTCAGGATCCAAATGCATTTGCAGTAGAAAAACAAATGGTTATTGAAAATGCAAGAGAGAAAATATTAAGCAACAAATCTCTTCAAGAAAAACTAGCAGAAAACATAAATAAGTTTTTGACTAGTGATAGTAGTGTTGCTCAAGTACCTAAGCAGACAGACAGCAACCCGACAGAGCCAGAAACGTCAATTGATGAACTGCTAGGCCTTCCGAGTGAAATCCATATGTCTGAAGAAGCCATACAAGATATTTTGGAGCAGACAGAATCAGACCCCGCCTTTCAGGCACTCTTTGATCTTTTTGACTATGGTAAAACAAAGAACAATAAAAATATGCCACAAATCTCTAGTCAACCTATGGAGACTAATTCTAATATAGTCTTGCCTGAAGAAACTAATCTAACAATTAAAAGTTCTTTTGAAACTGAAGAATCAGATACAGCTGGAGAGTCTTTGAATATCATTCCTGGTCCTCAGGAAAGGAAAACTCAAACCAGTTTAATGTCTCCTGGTAGACGTAAAAGTGAATCACAAAAGAAGAGTCTCACATCATCTGGACCGCATTCATCAAGGAATTTTCAGGATCCAAATGCATTTGCAGTAGAAAAACAAATGGTTATTGAAAATGCAAGAGAGAAAATATTAAGCAACAAATCTCTTCAAGAAAAACTAGCAGAAAACATAAATAAGTTTTTGACTAGTGATAGTAGTGTTGCTCAAGTACCTAAGCAGACAGACAGCAACCCGACAGAGCCAGAAACGTCAATTGATGAACTGCTAGGCCTTCCGAGTGAAATCCATATGTCTGAAGAAGCCATACAAGATATTTTGGAGCAGACAGAATCAGACCCCGCCTTTCAGGCACTCTTTGATCTTTTTGACTATGGTAAAACAAAGAACAATAAAAATATGCCACAAATCTCTAGTCAACCTATGGAGACTAATTCTAATATAGTCTTGCCTGAAGAAACTAATCTAACAATTAAAAGTTCTTTTGAAACTGAAGAATCA
Peptide sequence:
MSPGRRKSESQKKSLTSSGPHSSRNFQDPNAFAVEKQMVIENAREKILSNKSLQEKLAENINKFLTSDSSVAQVPKQTDSNPTEPETSIDELLGLPSEIHMSEEAIQDILEQTESDPAFQALFDLFDYGKTKNNKNMPQISSQPMETNSNIVLPEETNLTIKSSFETEESDTAGESLNIIPGPQERKTQTSLMSPGRRKSESQKKSLTSSGPHSSRNFQDPNAFAVEKQMVIENAREKILSNKSLQEKLAENINKFLTSDSSVAQVPKQTDSNPTEPETSIDELLGLPSEIHMSEEAIQDILEQTESDPAFQALFDLFDYGKTKNNKNMPQISSQPMETNSNIVLPEETNLTIKSSFETEES
IRESfinder result
IRESfinder score
0.750131013
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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