top of page
mmu_circSkp1_456
Basic information of circular RNA
PanCircBase ID:
mmu_circSkp1_456
mm39_Chr. Position ID:
chr11|52127663|52135948|+
Gene name:
Skp1
Transcript:
ENSMUST00000037324.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
2,3,4,5
Exon/intron offsets:
0,5750,6778,8144
Genomic length:
8285
Exon/intron sizes in nt:
97,74,144,141
Flanking exon/introns:
chr11:52122945-52127663|chr11:52135948-52136811
Splice length:
456
Other database IDs:
circBase: mmu_circ_0003111, CIRCpedia: MMU_CIRCpedia_22344, circAtlas: mmu-Skp1a_0002
circBase: hsa_circ_0003711, circAtlas: hsa-SKP1_0005, CIRCpedia: HSA_CIRCpedia_50196
Human Ortholog IDs:
Mature spliced Sequence:
ATGCCTACGATAAAGTTGCAGAGTTCTGATGGAGAGATATTTGAAGTTGATGTAGAAATTGCCAAACAATCTGTGACTATCAAGACCATGCTGGAAGATTTGGGAATGGATGATGAAGGAGATGATGATCCTGTTCCTTTACCAAATGTTAATGCAGCAATTCTAAAGAAGGTCATTCAGTGGTGCACCCACCACAAAGATGACCCTCCTCCTCCTGAGGATGATGAAAACAAAGAAAAGCGGACAGATGATATTCCTGTTTGGGACCAAGAATTCCTGAAAGTTGACCAAGGAACACTTTTTGAACTTATTCTGGCTGCAAACTACTTAGACATCAAAGGTTTGCTTGATGTCACATGCAAGACTGTGGCCAATATGATTAAGGGGAAAACTCCTGAGGAGATTCGTAAAACCTTCAATATCAAAAATGACTTTACTGAAGAGGAAGAGGCCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGGGAAAACTCCTGAGGA
57.87
AGCATGGTCTTGATAGTCACAGA
59.23
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGGGAAAACTCCTGAGGA
57.87
CAGCATGGTCTTGATAGTCACA
58.13
168
PCR template sequence:
ATGCAAGACTGTGGCCAATATGATTAAGGGGAAAACTCCTGAGGAGATTCGTAAAACCTTCAATATCAAAAATGACTTTACTGAAGAGGAAGAGGCCCAGATGCCTACGATAAAGTTGCAGAGTTCTGATGGAGAGATATTTGAAGTTGATGTAGAAATTGCCAAACAATCTGTGACTATCAAGACCATGCTGGAAGATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(1), mmu-miR-431-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGAAGAGGCCCAGATGCCTACGATAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSKP1_456_ORF_1
1.0936
0.310777141
0.990254902
912
ORF sequence:
ATGCCTACGATAAAGTTGCAGAGTTCTGATGGAGAGATATTTGAAGTTGATGTAGAAATTGCCAAACAATCTGTGACTATCAAGACCATGCTGGAAGATTTGGGAATGGATGATGAAGGAGATGATGATCCTGTTCCTTTACCAAATGTTAATGCAGCAATTCTAAAGAAGGTCATTCAGTGGTGCACCCACCACAAAGATGACCCTCCTCCTCCTGAGGATGATGAAAACAAAGAAAAGCGGACAGATGATATTCCTGTTTGGGACCAAGAATTCCTGAAAGTTGACCAAGGAACACTTTTTGAACTTATTCTGGCTGCAAACTACTTAGACATCAAAGGTTTGCTTGATGTCACATGCAAGACTGTGGCCAATATGATTAAGGGGAAAACTCCTGAGGAGATTCGTAAAACCTTCAATATCAAAAATGACTTTACTGAAGAGGAAGAGGCCCAGATGCCTACGATAAAGTTGCAGAGTTCTGATGGAGAGATATTTGAAGTTGATGTAGAAATTGCCAAACAATCTGTGACTATCAAGACCATGCTGGAAGATTTGGGAATGGATGATGAAGGAGATGATGATCCTGTTCCTTTACCAAATGTTAATGCAGCAATTCTAAAGAAGGTCATTCAGTGGTGCACCCACCACAAAGATGACCCTCCTCCTCCTGAGGATGATGAAAACAAAGAAAAGCGGACAGATGATATTCCTGTTTGGGACCAAGAATTCCTGAAAGTTGACCAAGGAACACTTTTTGAACTTATTCTGGCTGCAAACTACTTAGACATCAAAGGTTTGCTTGATGTCACATGCAAGACTGTGGCCAATATGATTAAGGGGAAAACTCCTGAGGAGATTCGTAAAACCTTCAATATCAAAAATGACTTTACTGAAGAGGAAGAGGCCCAG
Peptide sequence:
MPTIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQMPTIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQ
IRESfinder result
IRESfinder score
0.438109648
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page