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mmu_circNdc80_776
Basic information of circular RNA
PanCircBase ID:
mmu_circNdc80_776
mm39_Chr. Position ID:
chr17|71806261|71815768|-
Gene name:
Ndc80
Transcript:
ENSMUST00000024851.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
16,15,14,13,12,11
Exon/intron offsets:
0,1005,2242,5499,7993,9301
Genomic length:
9507
Exon/intron sizes in nt:
1,03,13,19,39,01,53,200
Flanking exon/introns:
chr17:71803348-71806261|chr17:71815768-71818339
Splice length:
776
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AACAAGAATGTGAAACTGTTAAACAGGAAAACACTCGACTACAGAGTATCGTTGATAACCAGAAGTATTCAGTCGCTGACATTGAGAGAATAAATCATGAGAAAAATGAATTGCAGCAGACTATTAATAAATTAACCAAAGACCTGGAAGCCGAACAGCAACAGATGTGGAATGAAGAATTAAAATACGCAAGAGGCAAAGAGGCGATTGAAGCGCAGCTAGCGGAGTACCACAAGTTGGCTAGAAAATTAAAGCTTATCCCCAAAGGTGCTGAGAATTCCAAAGGTTACGACTTTGAAATTAAGTTTAATCCTGAGGCGGGTGCCAACTGCCTTGTCAAATACAGGACTCAAGTGTATGCACCGCTCAAAGAGCTCTTGAATGAAAGCGAAGAAGAAATTAACAAAGCTCTGAATAAAAAGAGGCATCTGGAGGATACTTTAGAACAACTGAACACCATGAAAACGGAAAGCAAGAACACTGTGAGGATGCTGAAGGAGGAGATTCAGAAACTGGATGACCTTCACCAGCAGGCAGTGAAGGAAGCTGAGGAAAAAGACAAGAAGAGTGCCAGTGAGCTTGAGTCCCTGGAGAAACACAAGCACCTGCTGGAGAGCGGGGTGAACGATGGCCTCAGCGAGGCCATGGATGAGTTGGACGCCGTCCAGCGGGAATACCAGCTAACTGTGAAGACCACAACTGAAGAAAGAAGAAAGGTGGAAAACAACTTACAACGTCTTTTGGAGATGGTCGCCACACACGTAGGGTCTTTGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCTAACTGTGAAGACCAC
58.58
TCAGCGACTGAATACTTCTGGT
59.17
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGCTAACTGTGAAGACCAC
58.58
GTCAGCGACTGAATACTTCTGG
58.82
180
PCR template sequence:
CCAGCTAACTGTGAAGACCACAACTGAAGAAAGAAGAAAGGTGGAAAACAACTTACAACGTCTTTTGGAGATGGTCGCCACACACGTAGGGTCTTTGGAGAACAAGAATGTGAAACTGTTAAACAGGAAAACACTCGACTACAGAGTATCGTTGATAACCAGAAGTATTCAGTCGCTGACATTGAGAGAATAAATCATGA
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-9-5p(1), mmu-miR-27a-3p(1), mmu-miR-138-5p(1), mmu-miR-433-3p(1), mmu-miR-370-3p(1), mmu-miR-324-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGGGTCTTTGGAGAACAAGAATGTGA
siRNA sets
CTTGTTCTCCAAAGACCCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNDC80_776_ORF_1
1.1439
0.309101025
0.960802501
705
ORF sequence:
ATGTGGAATGAAGAATTAAAATACGCAAGAGGCAAAGAGGCGATTGAAGCGCAGCTAGCGGAGTACCACAAGTTGGCTAGAAAATTAAAGCTTATCCCCAAAGGTGCTGAGAATTCCAAAGGTTACGACTTTGAAATTAAGTTTAATCCTGAGGCGGGTGCCAACTGCCTTGTCAAATACAGGACTCAAGTGTATGCACCGCTCAAAGAGCTCTTGAATGAAAGCGAAGAAGAAATTAACAAAGCTCTGAATAAAAAGAGGCATCTGGAGGATACTTTAGAACAACTGAACACCATGAAAACGGAAAGCAAGAACACTGTGAGGATGCTGAAGGAGGAGATTCAGAAACTGGATGACCTTCACCAGCAGGCAGTGAAGGAAGCTGAGGAAAAAGACAAGAAGAGTGCCAGTGAGCTTGAGTCCCTGGAGAAACACAAGCACCTGCTGGAGAGCGGGGTGAACGATGGCCTCAGCGAGGCCATGGATGAGTTGGACGCCGTCCAGCGGGAATACCAGCTAACTGTGAAGACCACAACTGAAGAAAGAAGAAAGGTGGAAAACAACTTACAACGTCTTTTGGAGATGGTCGCCACACACGTAGGGTCTTTGGAGAACAAGAATGTGAAACTGTTAAACAGGAAAACACTCGACTACAGAGTATCGTTGATAACCAGAAGTATTCAGTCGCTGACATTGAGAGAATAA
Peptide sequence:
MWNEELKYARGKEAIEAQLAEYHKLARKLKLIPKGAENSKGYDFEIKFNPEAGANCLVKYRTQVYAPLKELLNESEEEINKALNKKRHLEDTLEQLNTMKTESKNTVRMLKEEIQKLDDLHQQAVKEAEEKDKKSASELESLEKHKHLLESGVNDGLSEAMDELDAVQREYQLTVKTTTEERRKVENNLQRLLEMVATHVGSLENKNVKLLNRKTLDYRVSLITRSIQSLTLRE
IRESfinder result
IRESfinder score
0.437480894
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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