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mmu_circTubd1_368
Basic information of circular RNA
PanCircBase ID:
mmu_circTubd1_368
mm39_Chr. Position ID:
chr11|86439608|86440297|+
Gene name:
Tubd1
Transcript:
ENSMUST00000167178.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
2,3
Exon/intron offsets:
0,541
Genomic length:
689
Exon/intron sizes in nt:
2,20,148
Flanking exon/introns:
chr11:86436162-86439608|chr11:86440297-86443613
Splice length:
368
Other database IDs:
circAtlas: mmu-Tubd1_0013
CIRCpedia: HSA_CIRCpedia_21691
Human Ortholog IDs:
Mature spliced Sequence:
GTGACCCACCCTCTGGTGTTTTAGACTAAGCCTCCTTTGTGGCTTGGCATGTCGATAGTGACAGTACAGCTGGGGCAGTGTGGCAACCAGATTGGCTTTGAAGTGTTTGATGCTTTATTTAGAGACTCACACTGTTCCCAGGGACTCTGTTCTAAGAGGGACAACGAGGCATATCAAGCTTCCTGCAGAGAAAGATTTTTCAGAGAGGAAGAAAATGGAGTTCCAGTTGCCCGGGCTGTTCTTGTTGACATGGAACCTAAAGTTATCAATCAAACACTATCAAAAGCTGCCCAGTCTGGCCGATGGAATTATGGTCAGCACACGAGTTTTTGTCAGAAACAAGGATCTGGGAACAACTGGGCATACGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAGTCTGGCCGATGGAATT
60.11
CAATCTGGTTGCCACACTGC
60.04
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCAAAAGCTGCCCAGTCTGG
60.54
GACATGCCAAGCCACAAAGG
60.04
142
PCR template sequence:
ATCAAACACTATCAAAAGCTGCCCAGTCTGGCCGATGGAATTATGGTCAGCACACGAGTTTTTGTCAGAAACAAGGATCTGGGAACAACTGGGCATACGGGTGACCCACCCTCTGGTGTTTTAGACTAAGCCTCCTTTGTGGCTTGGCATGTCGATAGTGACAGTACAGCTGGGGCAGTGTGGCAACCAGATTGGCTTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-324-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTGGGCATACGGGTGACCCACCCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTUBD1_368_ORF_1
0.7193
0.015638517
0.179363239
324
ORF sequence:
ATGTCGATAGTGACAGTACAGCTGGGGCAGTGTGGCAACCAGATTGGCTTTGAAGTGTTTGATGCTTTATTTAGAGACTCACACTGTTCCCAGGGACTCTGTTCTAAGAGGGACAACGAGGCATATCAAGCTTCCTGCAGAGAAAGATTTTTCAGAGAGGAAGAAAATGGAGTTCCAGTTGCCCGGGCTGTTCTTGTTGACATGGAACCTAAAGTTATCAATCAAACACTATCAAAAGCTGCCCAGTCTGGCCGATGGAATTATGGTCAGCACACGAGTTTTTGTCAGAAACAAGGATCTGGGAACAACTGGGCATACGGGTGA
Peptide sequence:
MSIVTVQLGQCGNQIGFEVFDALFRDSHCSQGLCSKRDNEAYQASCRERFFREEENGVPVARAVLVDMEPKVINQTLSKAAQSGRWNYGQHTSFCQKQGSGNNWAYG
IRESfinder result
IRESfinder score
0.722592754
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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