top of page
mmu_circNup54_685
Basic information of circular RNA
PanCircBase ID:
mmu_circNup54_685
mm39_Chr. Position ID:
chr5|92565311|92572329|-
Gene name:
Nup54
Transcript:
ENSMUST00000038514.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
11,10,9,8,7,6
Exon/intron offsets:
0,328,2064,5029,5524,6821
Genomic length:
7018
Exon/intron sizes in nt:
1,11,12,01,08,94,55,190
Flanking exon/introns:
chr5:92564197-92565311|chr5:92572329-92573481
Splice length:
685
Other database IDs:
CIRCpedia: MMU_CIRCpedia_37282
Human Ortholog IDs:
Mature spliced Sequence:
GACGGAAGTTGTCATTTATGTTGTTGAGCGTTCTCCAAATGGCACCTCGAGAAGAGTTCCAGCGACAACACTGTATGCCCACTTTGAGCAAGCCAACATTAAAGCCCAGCTGCAGCAGCTTGGGGTGACCCTTTCTATGACCAGGACAGAGCTGTCTCCCGCTCAGATCAAGCAGCTCTTACAAAACCCTCCCGCAGGTGTTGATCCTATTATTTGGGAACAGGCCAAGGTGGATAACCCAGACTCTGAAAAGTTAATTCCTGTACCAATGGTGGGTTTCAAAGAATTGCTTCGAAGACTGAAGGTTCAAGATCAGATGACTAAGCAGCATCAGACCAGACTAGATATCATATCTGAAGATATTAGTGAACTGCAAAAAAATCAAACTACGACTATGGCCAAAATAGCACAATACAAGAGGAAACTGATGGAGCTCTCCCACAGGACCTTACAGGTCCTAATCAAACAGGAAATCCAGAGGAAGAGTGGCTATGCGATCCAGGCTGATGAAGAGCAGTTGCGGGTTCAGCTAGATACTATTCAAGGGGAACTGAATGCGCCCACTCAGTTCAAAGGTCGGCTGAATGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACTACATAGATGCAGACCTGTTACGAGAAATCAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCCAGATCAGGATGCAG
59.16
GGAACTCTTCTCGAGGTGCC
60.11
152
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCCAGATCAGGATGCAG
59.16
CGCTGGAACTCTTCTCGAGG
60.18
156
PCR template sequence:
TGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACTACATAGATGCAGACCTGTTACGAGAAATCAAGCAGGACGGAAGTTGTCATTTATGTTGTTGAGCGTTCTCCAAATGGCACCTCGAGAAGAGTTCCAGCGACAACACTGTATGCCCACTTTGAGCAAGCCAACATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-434-3p(1), mmu-miR-194-5p(1), mmu-miR-129-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAATCAAGCAGGACGGAAGTTGTC
siRNA sets
AACTTCCGTCCTGCTTGAT, CAACTTCCGTCCTGCTTGA, TTCCGTCCTGCTTGATTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUP54_685_ORF_1
1.2207
0.250964081
0.959824356
714
ORF sequence:
ATGCAGACCTGTTACGAGAAATCAAGCAGGACGGAAGTTGTCATTTATGTTGTTGAGCGTTCTCCAAATGGCACCTCGAGAAGAGTTCCAGCGACAACACTGTATGCCCACTTTGAGCAAGCCAACATTAAAGCCCAGCTGCAGCAGCTTGGGGTGACCCTTTCTATGACCAGGACAGAGCTGTCTCCCGCTCAGATCAAGCAGCTCTTACAAAACCCTCCCGCAGGTGTTGATCCTATTATTTGGGAACAGGCCAAGGTGGATAACCCAGACTCTGAAAAGTTAATTCCTGTACCAATGGTGGGTTTCAAAGAATTGCTTCGAAGACTGAAGGTTCAAGATCAGATGACTAAGCAGCATCAGACCAGACTAGATATCATATCTGAAGATATTAGTGAACTGCAAAAAAATCAAACTACGACTATGGCCAAAATAGCACAATACAAGAGGAAACTGATGGAGCTCTCCCACAGGACCTTACAGGTCCTAATCAAACAGGAAATCCAGAGGAAGAGTGGCTATGCGATCCAGGCTGATGAAGAGCAGTTGCGGGTTCAGCTAGATACTATTCAAGGGGAACTGAATGCGCCCACTCAGTTCAAAGGTCGGCTGAATGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACTACATAGATGCAGACCTGTTACGAGAAATCAAGCAG
Peptide sequence:
MQTCYEKSSRTEVVIYVVERSPNGTSRRVPATTLYAHFEQANIKAQLQQLGVTLSMTRTELSPAQIKQLLQNPPAGVDPIIWEQAKVDNPDSEKLIPVPMVGFKELLRRLKVQDQMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLMELSHRTLQVLIKQEIQRKSGYAIQADEEQLRVQLDTIQGELNAPTQFKGRLNELMSQIRMQNHFGAVKSEEKYYIDADLLREIKQ
IRESfinder result
IRESfinder score
0.399503494
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page