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mmu_circDnajc3_360
Basic information of circular RNA
PanCircBase ID:
mmu_circDnajc3_360
mm39_Chr. Position ID:
chr14|119209774|119212676|+
Gene name:
Dnajc3
Transcript:
ENSMUST00000022734.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
8,9,10
Exon/intron offsets:
0,330,2769
Genomic length:
2902
Exon/intron sizes in nt:
106,121,133
Flanking exon/introns:
chr14:119208214-119209774|chr14:119212676-119214121
Splice length:
360
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
ATACACAGATGCAACCAGCAAATATGAATCAGTCATGAAAACAGAGCCCAGTGTTGCTGAGTACACAGTGCGCTCGAAGGAGAGGATCTGCCACTGCTTCTCTAAGGATGAGAAGCCCGTGGAAGCCATTAGGATATGTTCTGAAGTTTTACAGATGGAGCCCGACAATGTGAATGCTCTGAAAGACCGAGCCGAGGCCTACTTAATAGAGGAAATGTACGATGAAGCCATTCAGGATTATGAAGCTGCTCAGGAGCACAATGAAAATGACCAGCAGATTCGGGAAGGCTTAGAGAAAGCCCAGCGGTTACTGAAGCAGTCACAGAAACGAGATTATTATAAAATCTTGGGAGTAAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAGAAAGCCCAGCGGTTACT
60.04
GCAGATCCTCTCCTTCGAGC
59.97
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGAAAGCCCAGCGGTTAC
60.04
GCAGATCCTCTCCTTCGAGC
59.97
160
PCR template sequence:
ATGAAAATGACCAGCAGATTCGGGAAGGCTTAGAGAAAGCCCAGCGGTTACTGAAGCAGTCACAGAAACGAGATTATTATAAAATCTTGGGAGTAAAAAGATACACAGATGCAACCAGCAAATATGAATCAGTCATGAAAACAGAGCCCAGTGTTGCTGAGTACACAGTGCGCTCGAAGGAGAGGATCTGCCACTGCTTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-335-3p(2), mmu-miR-23b-3p(1), mmu-miR-135a-5p(1), mmu-miR-23a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGGAGTAAAAAGATACACAGATGCA
siRNA sets
CTGTGTATCTTTTTACTCC, ATCTGTGTATCTTTTTACT, TGTGTATCTTTTTACTCCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDNAJC3_360_ORF_1
0.8211
0.395532557
0.943752729
684
ORF sequence:
ATGAAAACAGAGCCCAGTGTTGCTGAGTACACAGTGCGCTCGAAGGAGAGGATCTGCCACTGCTTCTCTAAGGATGAGAAGCCCGTGGAAGCCATTAGGATATGTTCTGAAGTTTTACAGATGGAGCCCGACAATGTGAATGCTCTGAAAGACCGAGCCGAGGCCTACTTAATAGAGGAAATGTACGATGAAGCCATTCAGGATTATGAAGCTGCTCAGGAGCACAATGAAAATGACCAGCAGATTCGGGAAGGCTTAGAGAAAGCCCAGCGGTTACTGAAGCAGTCACAGAAACGAGATTATTATAAAATCTTGGGAGTAAAAAGATACACAGATGCAACCAGCAAATATGAATCAGTCATGAAAACAGAGCCCAGTGTTGCTGAGTACACAGTGCGCTCGAAGGAGAGGATCTGCCACTGCTTCTCTAAGGATGAGAAGCCCGTGGAAGCCATTAGGATATGTTCTGAAGTTTTACAGATGGAGCCCGACAATGTGAATGCTCTGAAAGACCGAGCCGAGGCCTACTTAATAGAGGAAATGTACGATGAAGCCATTCAGGATTATGAAGCTGCTCAGGAGCACAATGAAAATGACCAGCAGATTCGGGAAGGCTTAGAGAAAGCCCAGCGGTTACTGAAGCAGTCACAGAAACGAGATTATTATAAAATCTTGGGAGTAAAA
Peptide sequence:
MKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVK
IRESfinder result
IRESfinder score
0.36102146
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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