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mmu_circHipk3_673
Basic information of circular RNA
PanCircBase ID:
mmu_circHipk3_673
mm39_Chr. Position ID:
chr2|104267341|104271709|-
Gene name:
Hipk3
Transcript:
ENSMUST00000028600.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,854,2233,3209,4248
Genomic length:
4368
Exon/intron sizes in nt:
1,24,15,71,85,87,120
Flanking exon/introns:
chr2:104265402-104267341|chr2:104271709-104276856
Splice length:
673
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216843, circAtlas: mmu-Hipk3_0004
circBase: hsa_circ_0021603, circAtlas: hsa-HIPK3_0004, CIRCpedia: HSA_CIRCpedia_4137
Human Ortholog IDs:
Mature spliced Sequence:
ATCCGATACATTTCTCAGACTCAAGGTTTACCAGGAGAGCAATTGTTGAATGTGGGTACAAAATCCACAAGATTTTTTTGCAGAGAAACAGATATGTCTCATTCTGGTTGGAGGTTAAAGACACTGGAAGAGCATGAGGCAGAGACAGGAATGAAGTCTAAAGAGGCCAGAAAGTACATATTCAACAGTCTGGACGATATAGTGCATGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAGGCGTTAACCACATCTGCTCACTCTGTTGTGCACCATGGCATACCTCTGCAGGCGGGGACTGCACAGTTCGGTTGTGGAGATGCTTTTCATCAGACCCTGATTATCTGTCCCCCAGCTATCCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTGCACCATGGCATACCT
59.96
TGCTCTCCTGGTAAACCTTGAG
59.7
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGTGCACCATGGCATACCT
59.96
TGCTCTCCTGGTAAACCTTGA
58.67
140
PCR template sequence:
GTTGTGCACCATGGCATACCTCTGCAGGCGGGGACTGCACAGTTCGGTTGTGGAGATGCTTTTCATCAGACCCTGATTATCTGTCCCCCAGCTATCCAAGATCCGATACATTTCTCAGACTCAAGGTTTACCAGGAGAGCAATTGTTGAATGTGGGTACAAAATCCACAAGATTTTTTTGCAGAGAAACAGATATGTCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-322-5p(1), mmu-miR-298-5p(1), mmu-miR-181b-5p(1), mmu-miR-5101(1), mmu-miR-539-5p(1), mmu-miR-202-3p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCAGCTATCCAAGATCCGATACATTT
siRNA sets
AAATGTATCGGATCTTGGA, ATCGGATCTTGGATAGCTG, AATGTATCGGATCTTGGAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHIPK3_673_ORF_1
0.8446
-0.011039573
0.806128706
717
ORF sequence:
ATGTCTCATTCTGGTTGGAGGTTAAAGACACTGGAAGAGCATGAGGCAGAGACAGGAATGAAGTCTAAAGAGGCCAGAAAGTACATATTCAACAGTCTGGACGATATAGTGCATGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAGGCGTTAACCACATCTGCTCACTCTGTTGTGCACCATGGCATACCTCTGCAGGCGGGGACTGCACAGTTCGGTTGTGGAGATGCTTTTCATCAGACCCTGATTATCTGTCCCCCAGCTATCCAAGATCCGATACATTTCTCAGACTCAAGGTTTACCAGGAGAGCAATTGTTGAATGTGGGTACAAAATCCACAAGATTTTTTTGCAGAGAAACAGATATGTCTCATTCTGGTTGGAGGTTAAAGACACTGGAAGAGCATGA
Peptide sequence:
MSHSGWRLKTLEEHEAETGMKSKEARKYIFNSLDDIVHVNTVMDLEGGDLLAEKADRREFVNLLKKMLLIDADLRITPIETLNHPFVNMKHLLDFPHSNHVKSCFHIMDICKSPSSCETNNHSKMSLLRPVASNGTAALAANFTKVGTLRSQALTTSAHSVVHHGIPLQAGTAQFGCGDAFHQTLIICPPAIQDPIHFSDSRFTRRAIVECGYKIHKIFLQRNRYVSFWLEVKDTGRA
IRESfinder result
IRESfinder score
0.662326626
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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