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mmu_circHnrnpu_1476
Basic information of circular RNA
PanCircBase ID:
mmu_circHnrnpu_1476
mm39_Chr. Position ID:
chr1|178158156|178163723|-
Gene name:
Hnrnpu
Transcript:
ENSMUST00000161769.8
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:
0,501,757,1243,1501,2405,2955,3295,5290,5455
Genomic length:
5567
Exon/intron sizes in nt:
25,51,69,12,91,20,26,40,00,00,00,00,00,000
Flanking exon/introns:
chr1:178157911-178158156|chr1:178163723-178164517
Splice length:
1476
Other database IDs:
CIRCpedia: MMU_CIRCpedia_222247, circAtlas: mmu-HNRNPU_0018
Human Ortholog IDs:
Mature spliced Sequence:
GAGACGGCAAAACAGAACAGAAAGGTGGAGATAAAAAGAGAGGCGTTAAAAGACCGCGAGAAGATCATGGCCGAGGGTATTTTGAGTACATCGAAGAAAACAAGTACAGCAGAGCCAAGTCTCCTCAGCCACCTGTTGAAGAAGAAGACGAACACTTCGATGACACAGTGGTTTGTCTTGATACTTATAATTGTGATCTGCATTTTAAAATCTCGAGAGACCGTCTGAGTGCTTCTTCCCTTACTATGGAGAGTTTTGCTTTCCTGTGGGCTGGAGGAAGAGCTTCCTACGGTGTGTCAAAAGGCAAAGTCTGCTTTGAGATGAAGGTAACAGAGAAGATTCCAGTAAGACACTTATATACAAAAGATATTGATATACATGAAGTTCGGATTGGCTGGTCACTAACCACAAGTGGAATGTTGCTTGGTGAAGAAGAATTTTCTTACGGGTATTCTCTGAAAGGAATAAAAACATGCAACTGTGAGACAGAAGATTATGGGGAGAAGTTTGATGAAAATGATGTGATTACATGCTTTGCTAACTTTGAAACTGATGAAGTTGAACTCTCTTATGCGAAGAATGGACAAGATCTTGGTGTTGCCTTTAAGATCAGTAAGGAAGTTCTTGCTGACCGGCCACTATTCCCACATGTTCTCTGCCATAACTGTGCAGTTGAATTTAATTTCGGTCAAAAGGAAAAGCCATACTTTCCAATACCTGAAGACTGTACTTTTATCCAAAATGTCCCCTTAGAGGACCGAGTTAGAGGACCAAAAGGACCTGAAGAGAAGAAGGATTGTGAGGTTGTAATGATGATTGGCTTGCCAGGAGCTGGAAAAACTACCTGGGTTACTAAACATGCAGCTGAAAACCCTGGGAAATACAACATTCTTGGAACAAATACGATTATGGACAAGATGATGGTGGCAGGTTTTAAGAAGCAAATGGCAGATACTGGAAAACTGAACACACTGTTGCAGAGAGCCCCACAGTGTCTTGGCAAGTTTATTGAAATTGCTGCCCGTAAGAAGCGAAATTTTATTCTGGATCAGACAAATGTGTCTGCTGCTGCCCAGAGAAGAAAAATGTGCCTGTTTGCAGGCTTCCAGCGGAAAGCTGTTGTAGTGTGCCCAAAAGATGAAGACTATAAGCAGAGGACACAGAAGAAGGCAGAAGTAGAGGGGAAGGACCTACCAGAACATGCTGTCCTCAAGATGAAAGGAAACTTCACCCTTCCAGAGGTTGCAGAATGCTTTGATGAAATAACCTATGTTGAACTTCAGAAAGAGGAAGCCCAAAAGCTTTTGGAGCAATATAAAGAAGAAAGCAAAAAGGCACTGCCACCAGAAAAGAAGCAAAACACTGGCTCAAAGAAAAGCAATAAGAATAAGAGTGGCAAGAACCAGTTCAACAGAGGTGGTGGCCATAGAGGCCGTGGAGGATTCAATATGCGAGGTGGCAATTTCAGAGGAGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTTCAACAGAGGTGGTGGC
60.18
CCCTCGGCCATGATCTTCTC
59.97
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGAGGTGGTGGCCATAGA
60.25
CCCTCGGCCATGATCTTCTC
59.97
143
PCR template sequence:
AGCAATAAGAATAAGAGTGGCAAGAACCAGTTCAACAGAGGTGGTGGCCATAGAGGCCGTGGAGGATTCAATATGCGAGGTGGCAATTTCAGAGGAGGAGGAGACGGCAAAACAGAACAGAAAGGTGGAGATAAAAAGAGAGGCGTTAAAAGACCGCGAGAAGATCATGGCCGAGGGTATTTTGAGTACATCGAAGAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
15
Interacting miRNAs (#binding sites)
mmu-miR-137-3p(1), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-199a-5p(1), mmu-miR-135a-5p(1), mmu-miR-34a-5p(1), mmu-miR-205-5p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-196a-5p(1), mmu-miR-335-3p(1), mmu-miR-1904(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTCAGAGGAGGAGGAGACGGCAAAAC
siRNA sets
TTTTGCCGTCTCCTCCTCC, TTTGCCGTCTCCTCCTCCT, GTTTTGCCGTCTCCTCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHNRNPU_1476_ORF_1
1.0073
0.153298856
0.999999945
2706
ORF sequence:
ATGGAGAGTTTTGCTTTCCTGTGGGCTGGAGGAAGAGCTTCCTACGGTGTGTCAAAAGGCAAAGTCTGCTTTGAGATGAAGGTAACAGAGAAGATTCCAGTAAGACACTTATATACAAAAGATATTGATATACATGAAGTTCGGATTGGCTGGTCACTAACCACAAGTGGAATGTTGCTTGGTGAAGAAGAATTTTCTTACGGGTATTCTCTGAAAGGAATAAAAACATGCAACTGTGAGACAGAAGATTATGGGGAGAAGTTTGATGAAAATGATGTGATTACATGCTTTGCTAACTTTGAAACTGATGAAGTTGAACTCTCTTATGCGAAGAATGGACAAGATCTTGGTGTTGCCTTTAAGATCAGTAAGGAAGTTCTTGCTGACCGGCCACTATTCCCACATGTTCTCTGCCATAACTGTGCAGTTGAATTTAATTTCGGTCAAAAGGAAAAGCCATACTTTCCAATACCTGAAGACTGTACTTTTATCCAAAATGTCCCCTTAGAGGACCGAGTTAGAGGACCAAAAGGACCTGAAGAGAAGAAGGATTGTGAGGTTGTAATGATGATTGGCTTGCCAGGAGCTGGAAAAACTACCTGGGTTACTAAACATGCAGCTGAAAACCCTGGGAAATACAACATTCTTGGAACAAATACGATTATGGACAAGATGATGGTGGCAGGTTTTAAGAAGCAAATGGCAGATACTGGAAAACTGAACACACTGTTGCAGAGAGCCCCACAGTGTCTTGGCAAGTTTATTGAAATTGCTGCCCGTAAGAAGCGAAATTTTATTCTGGATCAGACAAATGTGTCTGCTGCTGCCCAGAGAAGAAAAATGTGCCTGTTTGCAGGCTTCCAGCGGAAAGCTGTTGTAGTGTGCCCAAAAGATGAAGACTATAAGCAGAGGACACAGAAGAAGGCAGAAGTAGAGGGGAAGGACCTACCAGAACATGCTGTCCTCAAGATGAAAGGAAACTTCACCCTTCCAGAGGTTGCAGAATGCTTTGATGAAATAACCTATGTTGAACTTCAGAAAGAGGAAGCCCAAAAGCTTTTGGAGCAATATAAAGAAGAAAGCAAAAAGGCACTGCCACCAGAAAAGAAGCAAAACACTGGCTCAAAGAAAAGCAATAAGAATAAGAGTGGCAAGAACCAGTTCAACAGAGGTGGTGGCCATAGAGGCCGTGGAGGATTCAATATGCGAGGTGGCAATTTCAGAGGAGGAGGAGACGGCAAAACAGAACAGAAAGGTGGAGATAAAAAGAGAGGCGTTAAAAGACCGCGAGAAGATCATGGCCGAGGGTATTTTGAGTACATCGAAGAAAACAAGTACAGCAGAGCCAAGTCTCCTCAGCCACCTGTTGAAGAAGAAGACGAACACTTCGATGACACAGTGGTTTGTCTTGATACTTATAATTGTGATCTGCATTTTAAAATCTCGAGAGACCGTCTGAGTGCTTCTTCCCTTACTATGGAGAGTTTTGCTTTCCTGTGGGCTGGAGGAAGAGCTTCCTACGGTGTGTCAAAAGGCAAAGTCTGCTTTGAGATGAAGGTAACAGAGAAGATTCCAGTAAGACACTTATATACAAAAGATATTGATATACATGAAGTTCGGATTGGCTGGTCACTAACCACAAGTGGAATGTTGCTTGGTGAAGAAGAATTTTCTTACGGGTATTCTCTGAAAGGAATAAAAACATGCAACTGTGAGACAGAAGATTATGGGGAGAAGTTTGATGAAAATGATGTGATTACATGCTTTGCTAACTTTGAAACTGATGAAGTTGAACTCTCTTATGCGAAGAATGGACAAGATCTTGGTGTTGCCTTTAAGATCAGTAAGGAAGTTCTTGCTGACCGGCCACTATTCCCACATGTTCTCTGCCATAACTGTGCAGTTGAATTTAATTTCGGTCAAAAGGAAAAGCCATACTTTCCAATACCTGAAGACTGTACTTTTATCCAAAATGTCCCCTTAGAGGACCGAGTTAGAGGACCAAAAGGACCTGAAGAGAAGAAGGATTGTGAGGTTGTAATGATGATTGGCTTGCCAGGAGCTGGAAAAACTACCTGGGTTACTAAACATGCAGCTGAAAACCCTGGGAAATACAACATTCTTGGAACAAATACGATTATGGACAAGATGATGGTGGCAGGTTTTAAGAAGCAAATGGCAGATACTGGAAAACTGAACACACTGTTGCAGAGAGCCCCACAGTGTCTTGGCAAGTTTATTGAAATTGCTGCCCGTAAGAAGCGAAATTTTATTCTGGATCAGACAAATGTGTCTGCTGCTGCCCAGAGAAGAAAAATGTGCCTGTTTGCAGGCTTCCAGCGGAAAGCTGTTGTAGTGTGCCCAAAAGATGAAGACTATAAGCAGAGGACACAGAAGAAGGCAGAAGTAGAGGGGAAGGACCTACCAGAACATGCTGTCCTCAAGATGAAAGGAAACTTCACCCTTCCAGAGGTTGCAGAATGCTTTGATGAAATAACCTATGTTGAACTTCAGAAAGAGGAAGCCCAAAAGCTTTTGGAGCAATATAAAGAAGAAAGCAAAAAGGCACTGCCACCAGAAAAGAAGCAAAACACTGGCTCAAAGAAAAGCAATAAGAATAAGAGTGGCAAGAACCAGTTCAACAGAGGTGGTGGCCATAGAGGCCGTGGAGGATTCAATATGCGAGGTGGCAATTTCAGAGGAGGA
Peptide sequence:
MESFAFLWAGGRASYGVSKGKVCFEMKVTEKIPVRHLYTKDIDIHEVRIGWSLTTSGMLLGEEEFSYGYSLKGIKTCNCETEDYGEKFDENDVITCFANFETDEVELSYAKNGQDLGVAFKISKEVLADRPLFPHVLCHNCAVEFNFGQKEKPYFPIPEDCTFIQNVPLEDRVRGPKGPEEKKDCEVVMMIGLPGAGKTTWVTKHAAENPGKYNILGTNTIMDKMMVAGFKKQMADTGKLNTLLQRAPQCLGKFIEIAARKKRNFILDQTNVSAAAQRRKMCLFAGFQRKAVVVCPKDEDYKQRTQKKAEVEGKDLPEHAVLKMKGNFTLPEVAECFDEITYVELQKEEAQKLLEQYKEESKKALPPEKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGGGDGKTEQKGGDKKRGVKRPREDHGRGYFEYIEENKYSRAKSPQPPVEEEDEHFDDTVVCLDTYNCDLHFKISRDRLSASSLTMESFAFLWAGGRASYGVSKGKVCFEMKVTEKIPVRHLYTKDIDIHEVRIGWSLTTSGMLLGEEEFSYGYSLKGIKTCNCETEDYGEKFDENDVITCFANFETDEVELSYAKNGQDLGVAFKISKEVLADRPLFPHVLCHNCAVEFNFGQKEKPYFPIPEDCTFIQNVPLEDRVRGPKGPEEKKDCEVVMMIGLPGAGKTTWVTKHAAENPGKYNILGTNTIMDKMMVAGFKKQMADTGKLNTLLQRAPQCLGKFIEIAARKKRNFILDQTNVSAAAQRRKMCLFAGFQRKAVVVCPKDEDYKQRTQKKAEVEGKDLPEHAVLKMKGNFTLPEVAECFDEITYVELQKEEAQKLLEQYKEESKKALPPEKKQNTGSKKSNKNKSGKNQFNRGGGHRGRGGFNMRGGNFRGG
IRESfinder result
IRESfinder score
0.501683002
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
RPF, cORF, m6A
mmu_circHnrnpu_001
Evidence
Peptide sequence:
MLNFRKRKPKSFWSNIKKKAKRHCHQKRSKTLAQRKAIRIRVARTSSTEVVAIEAVEDSICEVAISEEEETAKQNRKVEIKREALKDREKIMAEGILSTSKKTSTAEPSLLSHLLKKKTNTSMTQWFVLILIIVICILKSRETV*
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