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mmu_circTimmdc1_255
Basic information of circular RNA
PanCircBase ID:
mmu_circTimmdc1_255
mm39_Chr. Position ID:
chr16|38331080|38338894|-
Gene name:
Timmdc1
Transcript:
ENSMUST00000002925.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
3,2
Exon/intron offsets:
0,7648
Genomic length:
7814
Exon/intron sizes in nt:
89,166
Flanking exon/introns:
chr16:38329268-38331080|chr16:38338894-38342702
Splice length:
255
Other database IDs:
circBase: hsa_circ_0066873, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_347500
Human Ortholog IDs:
Mature spliced Sequence:
TGAACAACAGAGATTCTCAAAGGAAATTGACTATATCTACAGGGCAGCAGTTTCAGCAGGCATCATTGGCTGGGCATATGGAGGAATACCTGCTTTTATTTATGCTAAAAAACGCTACATTGAACAGAGCCAAGCGGAGATTTATCATAACCGATTTGATGCTGTGCAAAGTGCACACCGTGCTGCCACAAGGGGCTTCATCCGGTATGGCTGGCGCTGGAGTTGGAGAACTGCAGTTTTCGTGACCATATTTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGGGGCTTCATCCGGTATG
59.53
CCTCCATATGCCCAGCCAAT
59.89
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAGGGGCTTCATCCGGTAT
59.53
CCTCCATATGCCCAGCCAAT
59.89
151
PCR template sequence:
TTGATGCTGTGCAAAGTGCACACCGTGCTGCCACAAGGGGCTTCATCCGGTATGGCTGGCGCTGGAGTTGGAGAACTGCAGTTTTCGTGACCATATTTAATGAACAACAGAGATTCTCAAAGGAAATTGACTATATCTACAGGGCAGCAGTTTCAGCAGGCATCATTGGCTGGGCATATGGAGGAATACCTGCTTTTATT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TGACCATATTTAATGAACAACAGAGA
siRNA sets
TTGTTCATTAAATATGGTC, TGTTGTTCATTAAATATGG, GTTGTTCATTAAATATGGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTIMMDC1_255_ORF_1
0.8863
0.027748627
0.152106621
246
ORF sequence:
ATGAACAACAGAGATTCTCAAAGGAAATTGACTATATCTACAGGGCAGCAGTTTCAGCAGGCATCATTGGCTGGGCATATGGAGGAATACCTGCTTTTATTTATGCTAAAAAACGCTACATTGAACAGAGCCAAGCGGAGATTTATCATAACCGATTTGATGCTGTGCAAAGTGCACACCGTGCTGCCACAAGGGGCTTCATCCGGTATGGCTGGCGCTGGAGTTGGAGAACTGCAGTTTTCGTGA
Peptide sequence:
MNNRDSQRKLTISTGQQFQQASLAGHMEEYLLLFMLKNATLNRAKRRFIITDLMLCKVHTVLPQGASSGMAGAGVGELQFS
IRESfinder result
IRESfinder score
0.567662456
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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