top of page
mmu_circHipk3_549
Basic information of circular RNA
PanCircBase ID:
mmu_circHipk3_549
mm39_Chr. Position ID:
chr2|104268195|104271709|-
Gene name:
Hipk3
Transcript:
ENSMUST00000028600.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,6,5,4
Exon/intron offsets:
0,1379,2355,3394
Genomic length:
3514
Exon/intron sizes in nt:
15,71,85,87,120
Flanking exon/introns:
chr2:104267465-104268195|chr2:104271709-104276856
Splice length:
549
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_119529
Human Ortholog IDs:
Mature spliced Sequence:
ATCCGATACATTTCTCAGACTCAAGGTTTACCAGGAGAGCAATTGTTGAATGTGGGTACAAAATCCACAAGATTTTTTTGCAGAGAAACAGATATGTCTCATTCTGGTTGGAGGTTAAAGACACTGGAAGAGCATGAGGCAGAGACAGGAATGAAGTCTAAAGAGGCCAGAAAGTACATATTCAACAGTCTGGACGATATAGTGCATGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCACTCTTACGACCAGTC
56.63
ACCCACATTCAACAATTGCTCT
58.77
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCACTCTTACGACCAGTC
56.63
ACCCACATTCAACAATTGCTCTC
59.74
140
PCR template sequence:
AAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAGATCCGATACATTTCTCAGACTCAAGGTTTACCAGGAGAGCAATTGTTGAATGTGGGTACAAAATCCACAAGATTTTTTTGCAGAGAAACAGATATGTCTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-miR-322-5p(1), mmu-miR-181b-5p(1), mmu-miR-5101(1), mmu-miR-539-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTAAGAAGTCAGATCCGATACATTT
siRNA sets
AAATGTATCGGATCTGACT, ATGTATCGGATCTGACTTC, TGTATCGGATCTGACTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHIPK3_549_ORF_1
0.932
0.015815309
0.977718907
1005
ORF sequence:
ATGTCTCATTCTGGTTGGAGGTTAAAGACACTGGAAGAGCATGAGGCAGAGACAGGAATGAAGTCTAAAGAGGCCAGAAAGTACATATTCAACAGTCTGGACGATATAGTGCATGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAGATCCGATACATTTCTCAGACTCAAGGTTTACCAGGAGAGCAATTGTTGAATGTGGGTACAAAATCCACAAGATTTTTTTGCAGAGAAACAGATATGTCTCATTCTGGTTGGAGGTTAAAGACACTGGAAGAGCATGAGGCAGAGACAGGAATGAAGTCTAAAGAGGCCAGAAAGTACATATTCAACAGTCTGGACGATATAGTGCATGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAG
Peptide sequence:
MSHSGWRLKTLEEHEAETGMKSKEARKYIFNSLDDIVHVNTVMDLEGGDLLAEKADRREFVNLLKKMLLIDADLRITPIETLNHPFVNMKHLLDFPHSNHVKSCFHIMDICKSPSSCETNNHSKMSLLRPVASNGTAALAANFTKVGTLRSQIRYISQTQGLPGEQLLNVGTKSTRFFCRETDMSHSGWRLKTLEEHEAETGMKSKEARKYIFNSLDDIVHVNTVMDLEGGDLLAEKADRREFVNLLKKMLLIDADLRITPIETLNHPFVNMKHLLDFPHSNHVKSCFHIMDICKSPSSCETNNHSKMSLLRPVASNGTAALAANFTKVGTLRSQ
IRESfinder result
IRESfinder score
0.673224847
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page