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mmu_ciHdhd5_2643
Basic information of circular RNA
PanCircBase ID:
mmu_ciHdhd5_2643
mm39_Chr. Position ID:
chr6|120495511|120498154|-
Gene name:
Hdhd5
Transcript:
ENSMUST00000075303.7
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
2643
Exon/intron sizes in nt:
2643
Flanking exon/introns:
chr6:120495498-120498154
Splice length:
2643
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATCCTTTCAGTTTGCTGTTCCGGTGGAGAGGAGGGTGAAGGCTTGGCGTGCCACAGTTGGGGCGGGATGTTGGGAAACAGGGATAAATGAATGCTTTGTATGGTCGGTCCTTGAGACTAGTGGTAACAGCCCACATCAGAACCGTGTGCCCAGATTAATGTACAGAGACCCCTGTCTTAACCTTGAGCAATCTTGATCTCTGTGTCTCCAGTAAAAACTCTAGAATCTCCAGGCCAATGACCCCTCTGGAGGCCGAATGACCATTTCACAGGGGCTACATATCAGATAACATTAGATTTTACACTATGATTTATAACAGTAGCAAAATTACAGTCATGAAATAGCAACAACAATAATTTTATGTTTGGGGGTCACCAGGACATGTGGAACCTGTATTAAAGGGTCACAGCGATAGGAAACTGAGAGCCACTGCTCTGAGCAGGTATGCCCTAAGTGTGGGAGCCTCCCTCTAGCCTCTATCCTTGCTTGTCAGCCCCTGCTTGGAATAGCGCATTGTTGGTCATGTGTACACAGAAAGCAAAGGACATGGTCCCTGTCTTCAGACAGCTTGTTCATGTGCCCTCGATGCATCCTGGACCCCATGTAGACTGTGCTCCAAGGCAGGCTGGGACCCAGGTAAGAACATGTGACTTACTCAGGAGAGTCGTACTTGGGAGGGAAACACCCACAAACAGCAAAGGAGTGTGTAAGAGAGCAGGTGTTATAGAGGAATGGAACTGATAGGATAAACATACATCATCAATGAGATTTAGTCACTTTCCGTACACAGTTGGAGCCGGGTAGTTGAACAGTGACCGTCTGCTGGTAGAGCGCCTAGAAACTCTGTAGCTGCTCAGTCCACACTGAGCCTCAGCATCCCAGCCTGGCCCTGAAAGCCCACGCGTTCCTGGAGAGAGCTTCAGTACTTGTTGGAATCCCTCAGATTTCTTATATCTTCAGAAAGTGGGGAGAGCCTTCCCCCTCAGTTAACCCTCTCTGATTCATGTTTCTTAGGTGAATGTGGGTCCAGTCAAGATGACAGTCATCACAGGGTGGGGGGAAGCAAGCTCATCTGTGAGGGCACTGTGACCGGGTCTGACCACCTGTGTGTGACCAGGTCTGACCACCTGTGTGTGACTGGGTCTGACCACCTGTGTGTGAGGTGAAAGGAGAGAACTGACTCCCACAGGTTGTTCTTTGACGTCCATAATCCCCACAAATAAATGTAATTAAAAACAAACAAACAAAAGATGAGCTGTCCCAGCACAGGGGCTGGGAATGAGCCTCAGGTGGAGAGTTGTGTGTCGTGCTTGAGGCCCTGGTTTGCATCTCAAGTGCCAGGAAGAAGAGAAGATGGCACGGGGCCAGGGCAGGTTCTGCAGGTAGAGCACTGGCTTCTAAGCTTAGCCACCTGAGTTAGATCCCCAGGTTCCACACAGTGGGGGGAGAGAATGGATTCCGAAGTTGCGCCCTTTCAGCCACTGTGCCCCTTCCCCAGCTAAATAAATGCATCTTAGAAGGTGAAAAGATGGGCTGGGGGATTGAGATTGGCTCCAGGTTTGAGCATTGGAGTGTAGAGGGGACACCTGGAGCAGCAGCTGCTGCAGCAGCCTTTAGCTTTAGAGGGTTGGGTGGTCCCCTGGGAGGTGGGAAGACAAGGTGTCAGTCAGAAGGAGCGGAATTGGGCATTAGAGGACAGAAAGGCAGGCTGGGCGTGGACAGTCTCGTCCTAAACTCAGAGCAGTGGAGAGCTGGTGCAGGCCTTACGACTGCCGGGCAAATCTGTTAGATTTGGGGGATACTGGTTTTGAGTATCATCTGAGACTGGTTAAGATGGGACGGAGTTAGGGACAGGAAGATGGAGGCAGCTCTTAGAGGAGAGCAGGCTGGAGTCGTCATGGTCTTCTGTGTGACGGCCCCTTCCTTGCTGAGTGGGGTTTGACTGTCAGTGTTGTAGTTTCCTCTGAGTATTTGTGACTGTTGTGTGACTTGTCCTGGGGAGATGCGAACAACCATTATGTAACCCAGATAGGGAAAGAAGGACCGACCCATTGGCTTAATGAGCCAGGCAGTTAGCTAGGGTGAAAGGCACACTTCAGAAAGTGCCATGGAGGCTGAATGGTGACTGGGGAGCCCCCGCACAGCTTGCAGGCAGCTTGGCCATGGGAGTGTCTCTTCCCCCAGAACCTTGTATAACCATATAGGGGGAGGGGACTTTAAGCAGCACAGGAGGGAGGTTGTGGCTCTGGTAACTTTCAGGGTCCCCACCTCCCTCCAGGAGGGAATGTTTCAATCCAGAGGAAATAGCTATTCACCAGTTACTTGATTTTGCCTAGCTCCTTGCAGCCCAGTACTGAGGTCATGTTACTCACGAGCACCAGTTTGAACGGCCCTGTGCATGGCATAAGCTCCCTGAGTACACAGTGGGGGGGTTGGCCTCTTCTTCTCTGGGTCTTGCTGGTGTAGATAGAGTTGGTACCAGGGGGTCGCACTGGTGTTGCTTGCGTCTGCCCTGTCTATGCAGTCCCAGCCTGCACTTGGTGCCTGCCTGCCATGGTCTGGACTGGGCTTGGTTCTGCCCTCTTGTCACCTGATATCTCTATAAAAGCATCATCCCAGAACTGTGTAGCTTTGCTTCCCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTTCTGCCCTCTTGTCAC
59.89
TCCCTGTTTCCCAACATCCC
59.59
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTGCCCTCTTGTCACCTG
59.6
TCCCTGTTTCCCAACATCCC
59.59
153
PCR template sequence:
TGCCTGCCTGCCATGGTCTGGACTGGGCTTGGTTCTGCCCTCTTGTCACCTGATATCTCTATAAAAGCATCATCCCAGAACTGTGTAGCTTTGCTTCCCTGTATCCTTTCAGTTTGCTGTTCCGGTGGAGAGGAGGGTGAAGGCTTGGCGTGCCACAGTTGGGGCGGGATGTTGGGAAACAGGGATAAATGAATGCTTTG
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-377-3p(5), mmu-miR-224-5p(2), mmu-miR-490-3p(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-375-3p(1), mmu-miR-26a-5p(1), mmu-miR-214-3p(1), mmu-miR-149-5p(1), mmu-miR-153-3p(1), mmu-miR-26b-5p(1), mmu-miR-212-3p(1), mmu-miR-183-5p(1), mmu-miR-541-5p(1), mmu-miR-383-5p(1), mmu-miR-342-3p(1), mmu-miR-5101(1), mmu-miR-484(1), mmu-miR-188-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCTTTGCTTCCCTGTATCCTTTCAGT
siRNA sets
TGAAAGGATACAGGGAAGC, GAAAGGATACAGGGAAGCA, AAAGGATACAGGGAAGCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHDHD5_2643_ORF_5
0.5658
-0.184815465
0.022507199
180
ORF sequence:
ATGGTCTGGACTGGGCTTGGTTCTGCCCTCTTGTCACCTGATATCTCTATAAAAGCATCATCCCAGAACTGTGTAGCTTTGCTTCCCTGTATCCTTTCAGTTTGCTGTTCCGGTGGAGAGGAGGGTGAAGGCTTGGCGTGCCACAGTTGGGGCGGGATGTTGGGAAACAGGGATAAATGA
Peptide sequence:
MVWTGLGSALLSPDISIKASSQNCVALLPCILSVCCSGGEEGEGLACHSWGGMLGNRDK
IRESfinder result
IRESfinder score
0.6762038
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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