top of page
mmu_circTnpo1_394
Basic information of circular RNA
PanCircBase ID:
mmu_circTnpo1_394
mm39_Chr. Position ID:
chr13|98982928|98986691|-
Gene name:
Tnpo1
Transcript:
ENSMUST00000109399.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
23,22,21,20
Exon/intron offsets:
0,907,2734,3687
Genomic length:
3763
Exon/intron sizes in nt:
143,75,100,76
Flanking exon/introns:
chr13:98981128-98982928|chr13:98986691-98989362
Splice length:
394
Other database IDs:
circBase: hsa_circ_0072950, circAtlas: hsa-TNPO1_0163, CIRCpedia: HSA_CIRCpedia_52502
Human Ortholog IDs:
Mature spliced Sequence:
CAATAACAATTGGTCGTCTTGGTTACGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTATAAGACCCTGGTGTACCTCTCTGAGAAACATAAGAGACAATGAAGAAAAAGATTCAGCATTCCGTGGGATTTGTACCATGATCAGTGTGAATCCCAGTGGCGTAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAACCCAAAAGATGATCTCAGAGACATGTTCTGTAAGATCCTTCATGGATTTAAAAACCAAGTTGGGGATGAAAATTGGAGGCGATTCTCTGACCAGTTTCCTCTTCCCTTAAAAGAGCGTCTTGCAGCTTTTTATGGTGTTTAATCTAATACACTTAAGCTGCAGTCCCAAAACTAGGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCGATTCTCTGACCAGTTTCC
59
GGCCACCTCTTGAGGACAAA
59.89
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGCGATTCTCTGACCAGTTTC
59
GGCCACCTCTTGAGGACAAA
59.89
147
PCR template sequence:
GGCGATTCTCTGACCAGTTTCCTCTTCCCTTAAAAGAGCGTCTTGCAGCTTTTTATGGTGTTTAATCTAATACACTTAAGCTGCAGTCCCAAAACTAGGGCAATAACAATTGGTCGTCTTGGTTACGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTATAAGACCCTGGTGTACCTCTCTGAGAAACATAAG
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-141-3p(1), mmu-miR-19b-3p(1), mmu-miR-540-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCAAAACTAGGGCAATAACAATTGG
siRNA sets
AATTGTTATTGCCCTAGTT, CAATTGTTATTGCCCTAGT, ATTGTTATTGCCCTAGTTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTNPO1_394_ORF_1
0.8341
-0.137338658
0.205983036
405
ORF sequence:
ATGGTGTTTAATCTAATACACTTAAGCTGCAGTCCCAAAACTAGGGCAATAACAATTGGTCGTCTTGGTTACGTTTGTCCTCAAGAGGTGGCCCCCATGCTACAGCAGTTTATAAGACCCTGGTGTACCTCTCTGAGAAACATAAGAGACAATGAAGAAAAAGATTCAGCATTCCGTGGGATTTGTACCATGATCAGTGTGAATCCCAGTGGCGTAATCCAAGATTTTATATTTTTTTGTGATGCTGTTGCATCATGGATTAACCCAAAAGATGATCTCAGAGACATGTTCTGTAAGATCCTTCATGGATTTAAAAACCAAGTTGGGGATGAAAATTGGAGGCGATTCTCTGACCAGTTTCCTCTTCCCTTAAAAGAGCGTCTTGCAGCTTTTTATGGTGTTTAA
Peptide sequence:
MVFNLIHLSCSPKTRAITIGRLGYVCPQEVAPMLQQFIRPWCTSLRNIRDNEEKDSAFRGICTMISVNPSGVIQDFIFFCDAVASWINPKDDLRDMFCKILHGFKNQVGDENWRRFSDQFPLPLKERLAAFYGV
IRESfinder result
IRESfinder score
0.813138163
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page