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mmu_ciHerpud2_2401
Basic information of circular RNA
PanCircBase ID:
mmu_ciHerpud2_2401
mm39_Chr. Position ID:
chr9|25059714|25062115|-
Gene name:
Herpud2
Transcript:
ENSMUST00000008573.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
2401
Exon/intron sizes in nt:
2401
Flanking exon/introns:
chr9:25044568-25062115
Splice length:
2401
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTGTAAAACTGGACGCAGCTGCTCTGACCTGCTTGTTGCCCCGTGAACCTGGTACTTCCCTTCTCCCAACCTGCCCCTTCCTCGGCAATCAAATAGCTCTTCATTCGAAATACTTTTGGTTCTGAGGTTGCAGGTGTCTCCTGAGTGATCCATCATTATCCTCCTAATGAGGTTCAGTTAATTAGTGAGTATACAGAAATACCAAGAGACAAGAATTTGCAGTTACGGCAAAGGGACCGTCTTCCATGGAACTTAAAGTCATCAAATGTGAATGTCAGATGCTATTTTTGTTTTTCAGATAAAGAATCACTGTCCATATTAGAACCCTTGTTGTTTTCTAGGCTCAGAAATTTGTTCCTGGTGAAGAGAATTTTTTTTTTCCTCTTGGAATAAGTATGTGACTTAGCGAAAATTATACTTTAACCATCACTTCATTGCCTGGTTCTAAGTTGCAAATTCACTTTGTTTCCCACCTCACTTCTCCTGAAGAGGATACACACATTGAGACAGATGCAGCCCTTCCACATAACCCAGTCATTGATGCCTGTTTTGTTTTCTGTTGTATCATCTGTTTGTCTCAACTCAAGTGTGGCTTTGTTTCCAGTTCTTAACTATATCTTGGTATTGGAAAGATAAACAGAATGGAGTCATTTGTCCCTTACTTCAGATTTGAAGGGATGTAGTTAGTAAGTCTTGGAATAGTTTGGAGAAGTATTTCATATAGAGGATATTAAAGTGACTTTCATGTTCTGTATTGTATACCTTTTTCATTCTTGACTAGTATTCAGCTAGTAAATCTTTTAAAATAATAAAGAGCCTTTTATTTTATGGTGGGAAATATTTTGGCATATTTACCACCAGCTGGTTGGTGGTGTGCCAGCTGCTTTTTAGGCCTGTTCTGTGCTCTGAAGTATGGAAGATGCTTGATTAGGAACTGTTAAGATGTTTATGAGTTAGAACCTTGTCTGTTGCAGTATTGTTTAAGATTTAAGCTTCCAGAATAACCACTGGATTGCTTTATTGCAAAAGCTGGAGGATGTTTTTTTAAAACTCATTTGGCATTAGCTGAGTTTGGGACACAAGTATTTTTAGTATATGGGGGGAATGCTAAGTTACTTAAGTATTTGGTACAAAGTACTTACAAAGAGCTTTTGCTTATTCAAAGCCTAAGTTTGACAGTTAAGATTTACACATTGAGGATAACAATTCACAAAGAAATTGAGATTTATGAGAATATTCTAGTATATATTTTTGATTTTCCAAATTTTAAAAATAGAAAGCAACCTTGTGGAAATAGTTGCACTTGAAAGGCATAAATTTCCACAGTACTGTTTAAAATACAGCCCAAAATTTTAAAGTGCATTCTTAAGTCTATATACATCTTTATAGTATATACATCATATATACCATATATATGATATGTACCCTACAGTGTACATATACTGTAAACTACTATTTTAAAGTACATTTTAAGCCTGTAAACACCTGTGTGGTATGTACTTGGGTGAGATCTATGTGTTATACTGTTACACTGTGAGTACTCTTGGTCTTCAGTGTGTGGATCAAGAATTTCCATTAAGCCTAATGTGTAATCTTAGCACTTGAGAATCTAGAAGCTGAGGATCAGCCTTCCAGAGTCATTTTAGCTACACATTGAGTTTGAACCTAACATGATTCTTTCCTCAAAACCAAACAAATTTAGTATTCTAAAATTTTTCTCTGCAAAACAAAAACACTATGTAAGATAGAAATGTGAAGCCTTTTTGTCTTATCAGCCCAGGGATAAGCCACCTTGAGGCTGGAGGTTTACCCTTGCACAGATAGTCACTAGTGGAGTACTGTTGCTGCTCCTTGGACACTTCTGCCTGAGGAGATCACTTGCTAGACTGTCTTTTCTGACATGTTTGCCTTATAGACACACTGGAGATTCTTTTGGAGGCTGAACCACATACTGTCATTAATGATTTAACCTGTAACATTTCTCCAGCAAGTTTTCTGAGTGGATTGTAGTATCCTGTCAAGTTCATTTCTAGGTTGAAAACTTTGTGTAATTATTAGACTTGACAGGTTTCTGTTCTGACTTATCGTTTGAGGTTACGTTGCATTATCACAGTTGTTGAGTAACTGTAGTAGTGGTACCTTATAGCTATAGAAGACATCAGTTTTAGAAGTTGGAGTCATAGACCTTGTCTTTGTAAGGTTATTTAGAATCCATACATTTTGTAGTTTAGATTATAACAGGAATTTGGATTTGTATGACTGTCCACAATGACTCACATTGGCTTTTTAAATGTTTTAAGTATTCTATTCTACATGGGTATGCACATGTGTGCATGCTGCACCTTCCTTTAGAGTTAAGGTCTTACTGTGTTGTACACCATGATCTCAAATTCCTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCATGCTGCACCTTCCTTTAG
59.87
GCAGGTTGGGAGAAGGGAAG
60.32
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCATGCTGCACCTTCCTTTAG
59.87
TTTGATTGCCGAGGAAGGGG
60.32
163
PCR template sequence:
AAGTATTCTATTCTACATGGGTATGCACATGTGTGCATGCTGCACCTTCCTTTAGAGTTAAGGTCTTACTGTGTTGTACACCATGATCTCAAATTCCTGGGTAAGTGTAAAACTGGACGCAGCTGCTCTGACCTGCTTGTTGCCCCGTGAACCTGGTACTTCCCTTCTCCCAACCTGCCCCTTCCTCGGCAATCAAATAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
33
Interacting miRNAs (#binding sites)
mmu-miR-101a-3p(2), mmu-miR-18a-5p(2), mmu-miR-301b-3p(2), mmu-miR-301a-3p(2), mmu-miR-224-5p(2), mmu-miR-15a-5p(1), mmu-miR-106a-5p(1), mmu-miR-32-5p(1), mmu-miR-7b-5p(1), mmu-miR-200b-3p(1), mmu-miR-103-3p(1), mmu-miR-200c-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-130a-3p(1), mmu-miR-7a-5p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-128-3p(1), mmu-miR-136-5p(1), mmu-miR-721(1), mmu-miR-511-3p(1), mmu-miR-340-5p(1), mmu-miR-107-3p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-5101(1), mmu-miR-532-5p(1), mmu-miR-466b-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCAAATTCCTGGGTAAGTGTAAAAC
siRNA sets
TTTACACTTACCCAGGAAT, GTTTTACACTTACCCAGGA, TTTTACACTTACCCAGGAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHERPUD2_2401_ORF_1
0.8166
-0.255607304
0.029418741
192
ORF sequence:
ATGACTGTCCACAATGACTCACATTGGCTTTTTAAATGTTTTAAGTATTCTATTCTACATGGGTATGCACATGTGTGCATGCTGCACCTTCCTTTAGAGTTAAGGTCTTACTGTGTTGTACACCATGATCTCAAATTCCTGGGTAAGTGTAAAACTGGACGCAGCTGCTCTGACCTGCTTGTTGCCCCGTGA
Peptide sequence:
MTVHNDSHWLFKCFKYSILHGYAHVCMLHLPLELRSYCVVHHDLKFLGKCKTGRSCSDLLVAP
IRESfinder result
IRESfinder score
0.902560623
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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