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mmu_circPum1_820
Basic information of circular RNA
PanCircBase ID:
mmu_circPum1_820
mm39_Chr. Position ID:
chr4|130445464|130468867|+
Gene name:
Pum1
Transcript:
ENSMUST00000030315.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
4,5,6,7,8
Exon/intron offsets:
0,1019,9844,12124,23309
Genomic length:
23403
Exon/intron sizes in nt:
109,179,167,271,94
Flanking exon/introns:
chr4:130428421-130445464|chr4:130468867-130471000
Splice length:
820
Other database IDs:
circBase: mmu_circ_0011250, circAtlas: mmu-Pum1_0017
circAtlas: hsa-PUM1_0021, CIRCpedia: HSA_CIRCpedia_170214
Human Ortholog IDs:
Mature spliced Sequence:
CAGCTCTTGCCAGGTAAAAAGTTTTGGGAAACAGATGAATCCAGCAAAGATGGACCAAAAGGAATATTCCTGGGTGATCAATGGCGAGACAGTGCCTGGGGAACATCAGATCATTCAGTTTCCCAGCCAATCATGGTGCAGAGAAGACCTGGTCAGAGTTTCCATGTGAACAGTGAGGTCAATTCTGTACTGTCCCCACGGTCGGAGAGTGGGGGACTAGGCGTTAGCATGGTGGAGTATGTGTTGAGCTCATCCCCGGGCGACTCCTGTCTAAGAAAAGGAGGATTTGGCCCAAGGGATGCAGACAGTGATGAAAACGACAAAGGTGAAAAGAAGAACAAGGGTACGTTTGATGGAGATAAGCTAGGAGATTTGAAGGAGGAGGGAGATGTGATGGACAAGACCAATGGTTTGCCAGTGCAGAATGGGATTGATGCAGACGTCAAAGATTTTAGCCGTACCCCTGGTAATTGCCAGAACTCTGCTAATGAAGTGGATCTTCTGGGTCCAAACCAGAATGGTTCTGAGGGCTTAGCCCAGCTGACCAGCACCAATGGTGCCAAGCCTGTGGAGGATTTCTCCAACATGGAGTCCCAGAGTGTCCCCTTGGACCCCATGGAACATGTGGGCATGGAGCCTCTGCAGTTTGATTATTCAGGCACGCAGGTACCTGTGGACTCTGCAGCAGCAACTGTGGGACTTTTTGACTACAATTCTCAACAACAGCTATTCCAAAGACCCAATGCACTTGCTGTTCAGCAGTTGACAGCTGCCCAGCAGCAGCAGTATGCACTTGCAGCAGCCCACCAGCCTCACATCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTCAGCAGTTGACAGC
60.04
GTCTCGCCATTGATCACCCA
60.11
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGTTCAGCAGTTGACAGC
60.04
TGTCTCGCCATTGATCACCC
60.11
161
PCR template sequence:
CAACAGCTATTCCAAAGACCCAATGCACTTGCTGTTCAGCAGTTGACAGCTGCCCAGCAGCAGCAGTATGCACTTGCAGCAGCCCACCAGCCTCACATCGCAGCTCTTGCCAGGTAAAAAGTTTTGGGAAACAGATGAATCCAGCAAAGATGGACCAAAAGGAATATTCCTGGGTGATCAATGGCGAGACAGTGCCTGGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-31-5p(1), mmu-miR-101a-3p(1), mmu-miR-324-5p(1), mmu-miR-539-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAGCCTCACATCGCAGCTCTTGCCAG
siRNA sets
CAAGAGCTGCGATGTGAGG, AAGAGCTGCGATGTGAGGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCPUM1_820_ORF_1
1.0923
0.28046084
0.982788946
852
ORF sequence:
ATGCACTTGCAGCAGCCCACCAGCCTCACATCGCAGCTCTTGCCAGGTAAAAAGTTTTGGGAAACAGATGAATCCAGCAAAGATGGACCAAAAGGAATATTCCTGGGTGATCAATGGCGAGACAGTGCCTGGGGAACATCAGATCATTCAGTTTCCCAGCCAATCATGGTGCAGAGAAGACCTGGTCAGAGTTTCCATGTGAACAGTGAGGTCAATTCTGTACTGTCCCCACGGTCGGAGAGTGGGGGACTAGGCGTTAGCATGGTGGAGTATGTGTTGAGCTCATCCCCGGGCGACTCCTGTCTAAGAAAAGGAGGATTTGGCCCAAGGGATGCAGACAGTGATGAAAACGACAAAGGTGAAAAGAAGAACAAGGGTACGTTTGATGGAGATAAGCTAGGAGATTTGAAGGAGGAGGGAGATGTGATGGACAAGACCAATGGTTTGCCAGTGCAGAATGGGATTGATGCAGACGTCAAAGATTTTAGCCGTACCCCTGGTAATTGCCAGAACTCTGCTAATGAAGTGGATCTTCTGGGTCCAAACCAGAATGGTTCTGAGGGCTTAGCCCAGCTGACCAGCACCAATGGTGCCAAGCCTGTGGAGGATTTCTCCAACATGGAGTCCCAGAGTGTCCCCTTGGACCCCATGGAACATGTGGGCATGGAGCCTCTGCAGTTTGATTATTCAGGCACGCAGGTACCTGTGGACTCTGCAGCAGCAACTGTGGGACTTTTTGACTACAATTCTCAACAACAGCTATTCCAAAGACCCAATGCACTTGCTGTTCAGCAGTTGACAGCTGCCCAGCAGCAGCAGTATGCACTTGCAGCAGCCCACCAGCCTCACATC
Peptide sequence:
MHLQQPTSLTSQLLPGKKFWETDESSKDGPKGIFLGDQWRDSAWGTSDHSVSQPIMVQRRPGQSFHVNSEVNSVLSPRSESGGLGVSMVEYVLSSSPGDSCLRKGGFGPRDADSDENDKGEKKNKGTFDGDKLGDLKEEGDVMDKTNGLPVQNGIDADVKDFSRTPGNCQNSANEVDLLGPNQNGSEGLAQLTSTNGAKPVEDFSNMESQSVPLDPMEHVGMEPLQFDYSGTQVPVDSAAATVGLFDYNSQQQLFQRPNALAVQQLTAAQQQQYALAAAHQPHI
IRESfinder result
IRESfinder score
0.558755652
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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