top of page
mmu_circNlk_561
Basic information of circular RNA
PanCircBase ID:
mmu_circNlk_561
mm39_Chr. Position ID:
chr11|78474148|78509156|-
Gene name:
Nlk
Transcript:
ENSMUST00000142739.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,3546,5982,7560,34952
Genomic length:
35008
Exon/intron sizes in nt:
102,210,86,107,56
Flanking exon/introns:
chr11:78465753-78474148|chr11:78509156-78517402
Splice length:
561
Other database IDs:
circAtlas: mmu-Nlk_0002
circBase: hsa_circ_0106439, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_19820
Human Ortholog IDs:
Mature spliced Sequence:
GTACTCTCTGCCCTTGACATACTCCAACCTCCACACATTGACTATTTTGAAGAAATATATGTTGTCACAGAATTGATGCAGAGTGATCTACATAAAATTATCGTCTCTCCTCAGCCACTCAGCTCGGATCATGTCAAAGTTTTTCTTTATCAGATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTGCATCGAGACATTAAGCCAGGGAACCTCCTTGTGAACAGCAATTGTGTTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAGGAATTGGATGAATCCCGTCATATGACTCAGGAAGTAGTTACTCAGTATTACCGGGCTCCGGAGATCCTGATGGGCAGCCGTCATTACAGCAATGCTATCGACATCTGGTCTGTCGGGTGCATCTTTGCAGAGCTACTGGGCCGAAGAATATTGTTTCAGGCGCAGAGTCCCATTCAGCAGTTGGATTTGATCACAGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACAGCTTGTGAAGGTGCTAAGGCACACATACTCAGGGGTCCTCATAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGATCTGTTGGGCACACC
60.25
CACTCTGCATCAATTCTGTGACA
59.25
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGATCTGTTGGGCACACC
60.25
TCACTCTGCATCAATTCTGTGAC
59
176
PCR template sequence:
GGATTTGATCACAGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACAGCTTGTGAAGGTGCTAAGGCACACATACTCAGGGGTCCTCATAAACAGGTACTCTCTGCCCTTGACATACTCCAACCTCCACACATTGACTATTTTGAAGAAATATATGTTGTCACAGAATTGATGCAGAGTGATCTACATAAAATTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-429-3p(1), mmu-miR-122-5p(1), mmu-miR-501-3p(1), mmu-miR-297a-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCTCATAAACAGGTACTCTCTGCCC
siRNA sets
GAGAGTACCTGTTTATGAG, AGAGAGTACCTGTTTATGA, AGAGTACCTGTTTATGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNLK_561_ORF_1
1.0653
0.103210536
0.990889971
1047
ORF sequence:
ATGCAGAGTGATCTACATAAAATTATCGTCTCTCCTCAGCCACTCAGCTCGGATCATGTCAAAGTTTTTCTTTATCAGATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTGCATCGAGACATTAAGCCAGGGAACCTCCTTGTGAACAGCAATTGTGTTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAGGAATTGGATGAATCCCGTCATATGACTCAGGAAGTAGTTACTCAGTATTACCGGGCTCCGGAGATCCTGATGGGCAGCCGTCATTACAGCAATGCTATCGACATCTGGTCTGTCGGGTGCATCTTTGCAGAGCTACTGGGCCGAAGAATATTGTTTCAGGCGCAGAGTCCCATTCAGCAGTTGGATTTGATCACAGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACAGCTTGTGAAGGTGCTAAGGCACACATACTCAGGGGTCCTCATAAACAGGTACTCTCTGCCCTTGACATACTCCAACCTCCACACATTGACTATTTTGAAGAAATATATGTTGTCACAGAATTGATGCAGAGTGATCTACATAAAATTATCGTCTCTCCTCAGCCACTCAGCTCGGATCATGTCAAAGTTTTTCTTTATCAGATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTGCATCGAGACATTAAGCCAGGGAACCTCCTTGTGAACAGCAATTGTGTTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAGGAATTGGATGAATCCCGTCATATGACTCAGGAAGTAGTTACTCAGTATTACCGGGCTCCGGAGATCCTGATGGGCAGCCGTCATTACAGCAATGCTATCGACATCTGGTCTGTCGGGTGCATCTTTGCAGAGCTACTGGGCCGAAGAATATTGTTTCAGGCGCAGAGTCCCATTCAGCAGTTGGATTTGATCACAGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACAGCTTGTGAAGGTGCTAAGGCACACATACTCAGGGGTCCTCATAAACAG
Peptide sequence:
MQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGILHRDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIFAELLGRRILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAKAHILRGPHKQVLSALDILQPPHIDYFEEIYVVTELMQSDLHKIIVSPQPLSSDHVKVFLYQILRGLKYLHSAGILHRDIKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQYYRAPEILMGSRHYSNAIDIWSVGCIFAELLGRRILFQAQSPIQQLDLITDLLGTPSLEAMRTACEGAKAHILRGPHKQ
IRESfinder result
IRESfinder score
0.720136871
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page