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mmu_circNup54_1337
Basic information of circular RNA
PanCircBase ID:
mmu_circNup54_1337
mm39_Chr. Position ID:
chr5|92565311|92578981|-
Gene name:
Nup54
Transcript:
ENSMUST00000038514.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
10
Exon/intron indexes:
11,10,9,8,7,6,5,4,3,2
Exon/intron offsets:
0,328,2064,5029,5524,6821,8170,10647,13348,13586
Genomic length:
13670
Exon/intron sizes in nt:
111,120,108,94,55,197,188,227,153,84
Flanking exon/introns:
chr5:92564197-92565311|chr5:92578981-92582862
Splice length:
1337
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34372, circAtlas: mmu-Nup54_0002
circBase: hsa_circ_0070032, circAtlas: hsa-NUP54_0002, CIRCpedia: HSA_CIRCpedia_49127
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGTTTGGAGGATTTGGAACAACAACTACAACTGCAGGCTCTGCCTTCAGCTTTTCAGCCCCAACAAACACAGGCAGTACAGGCCTTCTCGGTGGCACTCAGAACAAAGGTTTTGGCTTTGGTACTGGTTTTGGCACAACGACGGGAACTGGCACTGGTTTAGGCACTGGCTTGGGAACCGGACTTGGATTTGGAGGATTTAATACCCAGCAGCAGCAGCAGCAGCAGCAGACTTCTTTAGGTGGTCTCTTCAGTCAGCCGACCCAGGCTCCTGCACAGTCTACCCAGCTCATCAACACTGCCAGCGCACTTTCTGCTCCAACGCTACTGGGGGATGAGAGAGACGCCATCTTGGCAAAGTGGAACCAGTTGCAGGCCTTCTGGGGAACAGGAAAAGGATATTTCAATAATAACATTCCTCCAGTGGAGTTTACCCAGGAGAATCCCTTTTGCCGGTTTAAGGCTGTAGGCTATAGTTGTATGCCCAATAATAAAGATGAAGATGGACTAGTAGTTTTAATTTTCAACAAAAAAGAAACAGATATTAGAAGCCAGCAACAGCAATTGGTAGAATCATTGCATAAAGTTTTGGGAGGAAACCAGACCCTTACGGTCAATGTGGAGGGCATTAAGACGTTGCCGGATGATCAGACGGAAGTTGTCATTTATGTTGTTGAGCGTTCTCCAAATGGCACCTCGAGAAGAGTTCCAGCGACAACACTGTATGCCCACTTTGAGCAAGCCAACATTAAAGCCCAGCTGCAGCAGCTTGGGGTGACCCTTTCTATGACCAGGACAGAGCTGTCTCCCGCTCAGATCAAGCAGCTCTTACAAAACCCTCCCGCAGGTGTTGATCCTATTATTTGGGAACAGGCCAAGGTGGATAACCCAGACTCTGAAAAGTTAATTCCTGTACCAATGGTGGGTTTCAAAGAATTGCTTCGAAGACTGAAGGTTCAAGATCAGATGACTAAGCAGCATCAGACCAGACTAGATATCATATCTGAAGATATTAGTGAACTGCAAAAAAATCAAACTACGACTATGGCCAAAATAGCACAATACAAGAGGAAACTGATGGAGCTCTCCCACAGGACCTTACAGGTCCTAATCAAACAGGAAATCCAGAGGAAGAGTGGCTATGCGATCCAGGCTGATGAAGAGCAGTTGCGGGTTCAGCTAGATACTATTCAAGGGGAACTGAATGCGCCCACTCAGTTCAAAGGTCGGCTGAATGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACTACATAGATGCAGACCTGTTACGAGAAATCAAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCCAGATCAGGATGCAG
59.16
TGTTGGGGCTGAAAAGCTGA
60.11
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCCCAGATCAGGATGCAG
59.16
GGCTGAAAAGCTGAAGGCAG
59.76
154
PCR template sequence:
TGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACTACATAGATGCAGACCTGTTACGAGAAATCAAGCAGGTGGGTTTGGAGGATTTGGAACAACAACTACAACTGCAGGCTCTGCCTTCAGCTTTTCAGCCCCAACAAACACAGGCAGTACAGGCCTTCTCGGTGGCAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-1a-3p(1), mmu-miR-150-5p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-106b-5p(1), mmu-miR-320-3p(1), mmu-miR-324-5p(1), mmu-miR-434-3p(1), mmu-miR-194-5p(1), mmu-miR-541-5p(1), mmu-miR-34b-5p(1), mmu-miR-325-3p(1), mmu-miR-129-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAAATCAAGCAGGTGGGTTTGGAGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUP54_1337_ORF_1
1.1355
0.193042041
0.993007881
1020
ORF sequence:
ATGCCCAATAATAAAGATGAAGATGGACTAGTAGTTTTAATTTTCAACAAAAAAGAAACAGATATTAGAAGCCAGCAACAGCAATTGGTAGAATCATTGCATAAAGTTTTGGGAGGAAACCAGACCCTTACGGTCAATGTGGAGGGCATTAAGACGTTGCCGGATGATCAGACGGAAGTTGTCATTTATGTTGTTGAGCGTTCTCCAAATGGCACCTCGAGAAGAGTTCCAGCGACAACACTGTATGCCCACTTTGAGCAAGCCAACATTAAAGCCCAGCTGCAGCAGCTTGGGGTGACCCTTTCTATGACCAGGACAGAGCTGTCTCCCGCTCAGATCAAGCAGCTCTTACAAAACCCTCCCGCAGGTGTTGATCCTATTATTTGGGAACAGGCCAAGGTGGATAACCCAGACTCTGAAAAGTTAATTCCTGTACCAATGGTGGGTTTCAAAGAATTGCTTCGAAGACTGAAGGTTCAAGATCAGATGACTAAGCAGCATCAGACCAGACTAGATATCATATCTGAAGATATTAGTGAACTGCAAAAAAATCAAACTACGACTATGGCCAAAATAGCACAATACAAGAGGAAACTGATGGAGCTCTCCCACAGGACCTTACAGGTCCTAATCAAACAGGAAATCCAGAGGAAGAGTGGCTATGCGATCCAGGCTGATGAAGAGCAGTTGCGGGTTCAGCTAGATACTATTCAAGGGGAACTGAATGCGCCCACTCAGTTCAAAGGTCGGCTGAATGAGCTGATGTCCCAGATCAGGATGCAGAATCATTTTGGAGCCGTGAAATCTGAAGAAAAGTACTACATAGATGCAGACCTGTTACGAGAAATCAAGCAGGTGGGTTTGGAGGATTTGGAACAACAACTACAACTGCAGGCTCTGCCTTCAGCTTTTCAGCCCCAACAAACACAGGCAGTACAGGCCTTCTCGGTGGCACTCAGAACAAAGGTTTTGGCTTTGGTACTGGTTTTGGCACAACGACGGGAACTGGCACTGGTTTAG
Peptide sequence:
MPNNKDEDGLVVLIFNKKETDIRSQQQQLVESLHKVLGGNQTLTVNVEGIKTLPDDQTEVVIYVVERSPNGTSRRVPATTLYAHFEQANIKAQLQQLGVTLSMTRTELSPAQIKQLLQNPPAGVDPIIWEQAKVDNPDSEKLIPVPMVGFKELLRRLKVQDQMTKQHQTRLDIISEDISELQKNQTTTMAKIAQYKRKLMELSHRTLQVLIKQEIQRKSGYAIQADEEQLRVQLDTIQGELNAPTQFKGRLNELMSQIRMQNHFGAVKSEEKYYIDADLLREIKQVGLEDLEQQLQLQALPSAFQPQQTQAVQAFSVALRTKVLALVLVLAQRRELALV
IRESfinder result
IRESfinder score
0.496404226
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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