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mmu_circNcl_525
Basic information of circular RNA
PanCircBase ID:
mmu_circNcl_525
mm39_Chr. Position ID:
chr1|86279919|86281577|-
Gene name:
Ncl
Transcript:
ENSMUST00000027438.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
11,10,9,8
Exon/intron offsets:
0,312,928,1534
Genomic length:
1658
Exon/intron sizes in nt:
1,22,12,41,55,124
Flanking exon/introns:
chr1:86279215-86279919|chr1:86281577-86282741
Splice length:
525
Other database IDs:
circAtlas: mmu-Ncl_0011
circBase: hsa_circ_0058670
Human Ortholog IDs:
Mature spliced Sequence:
TTCGAGCTGCAAGAACACTTCTAGCCAAAAACCTCTCTTTCAACATCACTGAGGATGAATTAAAGGAAGTGTTTGAAGACGCCATGGAGATCAGATTAGTCAGCCAGGATGGGAAAAGTAAAGGGATTGCTTATATTGAATTTAAGTCTGAAGCTGATGCAGAGAAAAATTTGGAAGAAAAGCAGGGGGCAGAAATTGATGGACGATCTGTTTCACTCTACTATACTGGAGAGAAAGGTCAAAGGCAAGAGAGAACTGGAAAGACCAGCACTTGGAGTGGTGAATCAAAGACTTTGGTTTTAAGTAACCTTTCCTACAGTGCAACAAAAGAAACTCTTGAGGAAGTATTTGAGAAAGCAACTTTTATCAAAGTGCCCCAGAACCCACATGGCAAACCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGGCAGAACAATCAGGCT
60.03
CTGATCTCCATGGCGTCTTCA
59.86
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAGGGCAGAACAATCAGGCT
60.03
TGATCTCCATGGCGTCTTCA
58.81
142
PCR template sequence:
TCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGTCTTCGAGCTGCAAGAACACTTCTAGCCAAAAACCTCTCTTTCAACATCACTGAGGATGAATTAAAGGAAGTGTTTGAAGACGCCATGGAGATCAGATTAGT
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-362-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTCGAGAAGTCTTCGAGCTGCAAG
siRNA sets
TTGCAGCTCGAAGACTTCT, CTTGCAGCTCGAAGACTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCL_525_ORF_1
0.9967
0.087327156
0.98042763
966
ORF sequence:
ATGGAGATCAGATTAGTCAGCCAGGATGGGAAAAGTAAAGGGATTGCTTATATTGAATTTAAGTCTGAAGCTGATGCAGAGAAAAATTTGGAAGAAAAGCAGGGGGCAGAAATTGATGGACGATCTGTTTCACTCTACTATACTGGAGAGAAAGGTCAAAGGCAAGAGAGAACTGGAAAGACCAGCACTTGGAGTGGTGAATCAAAGACTTTGGTTTTAAGTAACCTTTCCTACAGTGCAACAAAAGAAACTCTTGAGGAAGTATTTGAGAAAGCAACTTTTATCAAAGTGCCCCAGAACCCACATGGCAAACCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGTCTTCGAGCTGCAAGAACACTTCTAGCCAAAAACCTCTCTTTCAACATCACTGAGGATGAATTAAAGGAAGTGTTTGAAGACGCCATGGAGATCAGATTAGTCAGCCAGGATGGGAAAAGTAAAGGGATTGCTTATATTGAATTTAAGTCTGAAGCTGATGCAGAGAAAAATTTGGAAGAAAAGCAGGGGGCAGAAATTGATGGACGATCTGTTTCACTCTACTATACTGGAGAGAAAGGTCAAAGGCAAGAGAGAACTGGAAAGACCAGCACTTGGAGTGGTGAATCAAAGACTTTGGTTTTAAGTAACCTTTCCTACAGTGCAACAAAAGAAACTCTTGAGGAAGTATTTGAGAAAGCAACTTTTATCAAAGTGCCCCAGAACCCACATGGCAAACCTAAAGGGTATGCATTTATAGAATTTGCTTCATTTGAAGATGCTAAAGAAGCTTTAAATTCCTGTAATAAAATGGAAATTGAGGGCAGAACAATCAGGCTGGAGTTGCAAGGATCCAATTCGAGAAGT
Peptide sequence:
MEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGQRQERTGKTSTWSGESKTLVLSNLSYSATKETLEEVFEKATFIKVPQNPHGKPKGYAFIEFASFEDAKEALNSCNKMEIEGRTIRLELQGSNSRSLRAARTLLAKNLSFNITEDELKEVFEDAMEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGQRQERTGKTSTWSGESKTLVLSNLSYSATKETLEEVFEKATFIKVPQNPHGKPKGYAFIEFASFEDAKEALNSCNKMEIEGRTIRLELQGSNSRS
IRESfinder result
IRESfinder score
0.666862793
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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