top of page
mmu_circKnstrn_331
Basic information of circular RNA
PanCircBase ID:
mmu_circKnstrn_331
mm39_Chr. Position ID:
chr2|118653900|118662108|+
Gene name:
Knstrn
Transcript:
ENSMUST00000134661.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
5,6,7,8
Exon/intron offsets:
0,273,5539,8133
Genomic length:
8208
Exon/intron sizes in nt:
106,94,56,75
Flanking exon/introns:
chr2:118649363-118653900|chr2:118662108-118664480
Splice length:
331
Other database IDs:
circBase: hsa_circ_0103433, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_14114
Human Ortholog IDs:
Mature spliced Sequence:
CTACAAACCGTTTAATAAGCAAAAACCGGAGGAGGAACTAAAGGATAAAAATGAGCTGCTGGAGGCTGTCAACAAGCAGTTACACCAGAAGCTGACAGAGACTCAGGGAGAGCTGAAGGACCTGACACAGAAAGTGGAGCTACTGGAGAAGTTTCAGGATAACTGCTTAGCACTTTTGGAGAGCAAAGGTCTCAACCCAGGCCAAGAGACCCTGGCATCAAAGCAGGAACCCACCACAGATCACACGGACTCCATGCTGCTGCTCGAAACTTTGAAAGACGAACTGAAGGTTTTCAATGAAACCGCCAAGAAGCAGATGGAGGAGCTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATCACACGGACTCCATGCTG
60.11
TGCTTGTTGACAGCCTCCAG
60.54
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATCACACGGACTCCATGCTG
60.11
CTGCTTGTTGACAGCCTCCA
60.54
171
PCR template sequence:
CACCACAGATCACACGGACTCCATGCTGCTGCTCGAAACTTTGAAAGACGAACTGAAGGTTTTCAATGAAACCGCCAAGAAGCAGATGGAGGAGCTACAGCTACAAACCGTTTAATAAGCAAAAACCGGAGGAGGAACTAAAGGATAAAAATGAGCTGCTGGAGGCTGTCAACAAGCAGTTACACCAGAAGCTGACAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-125b-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1), mmu-miR-207(1), mmu-miR-1199-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAGGAGCTACAGCTACAAACCGTTT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKNSTRN_331_ORF_1
1.2121
0.399964107
0.781075145
366
ORF sequence:
ATGAAACCGCCAAGAAGCAGATGGAGGAGCTACAGCTACAAACCGTTTAATAAGCAAAAACCGGAGGAGGAACTAAAGGATAAAAATGAGCTGCTGGAGGCTGTCAACAAGCAGTTACACCAGAAGCTGACAGAGACTCAGGGAGAGCTGAAGGACCTGACACAGAAAGTGGAGCTACTGGAGAAGTTTCAGGATAACTGCTTAGCACTTTTGGAGAGCAAAGGTCTCAACCCAGGCCAAGAGACCCTGGCATCAAAGCAGGAACCCACCACAGATCACACGGACTCCATGCTGCTGCTCGAAACTTTGAAAGACGAACTGAAGGTTTTCAATGAAACCGCCAAGAAGCAGATGGAGGAGCTACAG
Peptide sequence:
MKPPRSRWRSYSYKPFNKQKPEEELKDKNELLEAVNKQLHQKLTETQGELKDLTQKVELLEKFQDNCLALLESKGLNPGQETLASKQEPTTDHTDSMLLLETLKDELKVFNETAKKQMEELQ
IRESfinder result
IRESfinder score
0.365923966
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page