top of page
mmu_circKnl1_1460
Basic information of circular RNA
PanCircBase ID:
mmu_circKnl1_1460
mm39_Chr. Position ID:
chr2|118906712|118933102|+
Gene name:
Knl1
Transcript:
ENSMUST00000099542.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
15
Exon/intron indexes:
9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Exon/intron offsets:
0,704,1666,5278,10328,11244,12567,17774,18034,18896,21186,23530,24481,25750,26267
Genomic length:
26390
Exon/intron sizes in nt:
1,39,68,99,11,69,11,17,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr2:118903100-118906712|chr2:118933102-118934458
Splice length:
1460
Other database IDs:
CIRCpedia: MMU_CIRCpedia_4667, circAtlas: mmu-Casc5_0006
Human Ortholog IDs:
Mature spliced Sequence:
ATTTTTGATAATCATATGGAAGAGGATATCAATAAAAATGTCAACAGTGTATTGCTGAAAAGCCTGAGCAGGACACCGTCTAGTTGCAGCAGCTCTCTGGATTCAATCAAGTCTGATGGACTCTCTCTGGATGTCAGCACACAGCGTAATAGCCAAATGGAATCACAGTTTCTTGGTGACACTATCTCTGAAGAGAGTTTGAAGGAGAAACTCAAGGATGGACAAATTACAATAAAGGAGTTCTTCATACTTCTTCAGGTCCACATCTTAATACAGAAACCTAGGCAGAGCACTCTCCCAGCCAAATTTACTATAAACACATTACCTACCACAGAAGATCTGATGTTGAGACAATATGTTTATGGACCCAGGATACAGATTTATAAAGAAGACTGTGAGCTTCTTCGACAAAAGATTGACGAATTAAAGATATCTGCATTGAACCAAAATAAACTATTGGCGGATGTAAATAGGAACTTGTGGGAAAAAGTGAAAGACTACTCTGATGAAGAGCTGAAGAACTATGGGATTTACCTTAACAAAATCAAATCACGTTATACCAAGATGACAAAAGTCTTCAATCACCAAGGAAAAGTGGCTCTGTATAACAAATTGGTGCATTCAGCTGAGAATGAGAAGAACAAACTTCAGATAAAAATAAATGAGATGGACACTATCCTCAAGAAGATCAATAACTGTCTCGCTGAAGTGGAAACAGAAACTAAGAATTTGGAGAATGAAGAGAAAAATGATGCCATGGAAGAATGGGATTCTGAAATGAGAGATGCAGAGAAAGAACTGGAACAGCTGAAAACTGAAGAAGAGGAGCTTCAGAGAAAGTTCTTAGAAGTAGAGACACAGAAAACGCAGACCCTTGCTCAGATAGAATTTATAAAAGAACAAACAACTAAAACTGAAGAATTACTGGATCAATTGAGTTTGTCTGAGTGGGATGTCATTGAGTGGAGTGATGATCAAGCTGTATTTACCTTTGTCTATGATTCAATAGAACTCATCATCACCTTTGGAGAGCCACTAGTTGGTCTCCCTTTTTTGGACAAGGCTTGCAGGAAGATTAATGCACTCAGTTTTCAGTCTCTGTTAGATGAAGATAAAGCTCCTCCCTCCTCCCTTTTAGTTCACAAGCTTATTTTTCAGTACATTGAGGAACAGGAATCCTGGAAGAAGAAATGCACAGCACAGCATCAGGTGCCCCAGATGCTTCAAGAACTCTCACTGGTAGTGAACCATTGTAGGCTTCTTGGAGAGGAGATCGAATTTTTAAAGCGATGGGGGCCAAATTATAGCCTAATGCATATAAATGTGAATAATACTGAATTGAGGCTTTTATTCTCCAGTTGTGCAGCATTTGCAAAGTTTGAGATAACTTTGTCTCCCTCGGCCCATTATCCCTTGGTCCCGTTACCGTTCACCATTCACAATCACATTGGGAAGACTGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTGGTCCCGTTACCGTTCA
59.97
AGAGCTGCTGCAACTAGACG
60.11
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCCGTTACCGTTCACCAT
60.04
AGAGCTGCTGCAACTAGACG
60.11
140
PCR template sequence:
GTGCAGCATTTGCAAAGTTTGAGATAACTTTGTCTCCCTCGGCCCATTATCCCTTGGTCCCGTTACCGTTCACCATTCACAATCACATTGGGAAGACTGGATTTTTGATAATCATATGGAAGAGGATATCAATAAAAATGTCAACAGTGTATTGCTGAAAAGCCTGAGCAGGACACCGTCTAGTTGCAGCAGCTCTCTGG
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-23b-3p(1), mmu-miR-7b-5p(1), mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-23a-3p(1), mmu-miR-325-3p(1), mmu-miR-1198-5p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
TTGGGAAGACTGGATTTTTGATAATC
siRNA sets
ATTATCAAAAATCCAGTCT, TCAAAAATCCAGTCTTCCC, TATCAAAAATCCAGTCTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCKNL1_1460_ORF_1
0.9596
0.070734162
0.999504036
1503
ORF sequence:
ATGGAAGAGGATATCAATAAAAATGTCAACAGTGTATTGCTGAAAAGCCTGAGCAGGACACCGTCTAGTTGCAGCAGCTCTCTGGATTCAATCAAGTCTGATGGACTCTCTCTGGATGTCAGCACACAGCGTAATAGCCAAATGGAATCACAGTTTCTTGGTGACACTATCTCTGAAGAGAGTTTGAAGGAGAAACTCAAGGATGGACAAATTACAATAAAGGAGTTCTTCATACTTCTTCAGGTCCACATCTTAATACAGAAACCTAGGCAGAGCACTCTCCCAGCCAAATTTACTATAAACACATTACCTACCACAGAAGATCTGATGTTGAGACAATATGTTTATGGACCCAGGATACAGATTTATAAAGAAGACTGTGAGCTTCTTCGACAAAAGATTGACGAATTAAAGATATCTGCATTGAACCAAAATAAACTATTGGCGGATGTAAATAGGAACTTGTGGGAAAAAGTGAAAGACTACTCTGATGAAGAGCTGAAGAACTATGGGATTTACCTTAACAAAATCAAATCACGTTATACCAAGATGACAAAAGTCTTCAATCACCAAGGAAAAGTGGCTCTGTATAACAAATTGGTGCATTCAGCTGAGAATGAGAAGAACAAACTTCAGATAAAAATAAATGAGATGGACACTATCCTCAAGAAGATCAATAACTGTCTCGCTGAAGTGGAAACAGAAACTAAGAATTTGGAGAATGAAGAGAAAAATGATGCCATGGAAGAATGGGATTCTGAAATGAGAGATGCAGAGAAAGAACTGGAACAGCTGAAAACTGAAGAAGAGGAGCTTCAGAGAAAGTTCTTAGAAGTAGAGACACAGAAAACGCAGACCCTTGCTCAGATAGAATTTATAAAAGAACAAACAACTAAAACTGAAGAATTACTGGATCAATTGAGTTTGTCTGAGTGGGATGTCATTGAGTGGAGTGATGATCAAGCTGTATTTACCTTTGTCTATGATTCAATAGAACTCATCATCACCTTTGGAGAGCCACTAGTTGGTCTCCCTTTTTTGGACAAGGCTTGCAGGAAGATTAATGCACTCAGTTTTCAGTCTCTGTTAGATGAAGATAAAGCTCCTCCCTCCTCCCTTTTAGTTCACAAGCTTATTTTTCAGTACATTGAGGAACAGGAATCCTGGAAGAAGAAATGCACAGCACAGCATCAGGTGCCCCAGATGCTTCAAGAACTCTCACTGGTAGTGAACCATTGTAGGCTTCTTGGAGAGGAGATCGAATTTTTAAAGCGATGGGGGCCAAATTATAGCCTAATGCATATAAATGTGAATAATACTGAATTGAGGCTTTTATTCTCCAGTTGTGCAGCATTTGCAAAGTTTGAGATAACTTTGTCTCCCTCGGCCCATTATCCCTTGGTCCCGTTACCGTTCACCATTCACAATCACATTGGGAAGACTGGATTTTTGATAATCATATGGAAGAGGATATCAATAAAAATGTCAACAGTGTATTGCTGA
Peptide sequence:
MEEDINKNVNSVLLKSLSRTPSSCSSSLDSIKSDGLSLDVSTQRNSQMESQFLGDTISEESLKEKLKDGQITIKEFFILLQVHILIQKPRQSTLPAKFTINTLPTTEDLMLRQYVYGPRIQIYKEDCELLRQKIDELKISALNQNKLLADVNRNLWEKVKDYSDEELKNYGIYLNKIKSRYTKMTKVFNHQGKVALYNKLVHSAENEKNKLQIKINEMDTILKKINNCLAEVETETKNLENEEKNDAMEEWDSEMRDAEKELEQLKTEEEELQRKFLEVETQKTQTLAQIEFIKEQTTKTEELLDQLSLSEWDVIEWSDDQAVFTFVYDSIELIITFGEPLVGLPFLDKACRKINALSFQSLLDEDKAPPSSLLVHKLIFQYIEEQESWKKKCTAQHQVPQMLQELSLVVNHCRLLGEEIEFLKRWGPNYSLMHINVNNTELRLLFSSCAAFAKFEITLSPSAHYPLVPLPFTIHNHIGKTGFLIIIWKRISIKMSTVYC
IRESfinder result
IRESfinder score
0.726143646
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page