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mmu_circDnajc1_733
Basic information of circular RNA
PanCircBase ID:
mmu_circDnajc1_733
mm39_Chr. Position ID:
chr2|18236514|18313760|-
Gene name:
Dnajc1
Transcript:
ENSMUST00000091418.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
9,8,7,6,5,4
Exon/intron offsets:
0,52919,62250,75269,76211,77080
Genomic length:
77246
Exon/intron sizes in nt:
12,01,64,91,94,98,166
Flanking exon/introns:
chr2:18227572-18236514|chr2:18313760-18321168
Splice length:
733
Other database IDs:
CIRCpedia: MMU_CIRCpedia_12444, circAtlas: mmu-Dnajc1_0004
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_66960
Human Ortholog IDs:
Mature spliced Sequence:
GTATGATGATGTTCTGATCAATGGACTTCCAGATTGGCGACAGCCTGTATTCTACTACAGGCGAGTGAGAAAAATGAGCAATGCTGAGCTGGCTTTGCTCTTGTTCATTATTCTCACAGTGGGTCACTATGCTGTGGTTTGGTCCATCTACCTGGAAAAGCAACTGGATGAACTGCTTGGTAGAAAAAAGAGAGAAAGGAAGAAGAAGACAGGAAGCAAGAGTGTGGACGCAGCAAAACTTGGTGCTTCTGAAAAGAACGAAAGATTGCTTATAAAACCACAATGGCATGATTTGCTTCCATGCAAACTGGGGATTTGGTTTTGCCTTACACTAAAAGCATTGCCTCATCTAATCCAGGATGCTGGGCAGTTTTATGCAAAATATAAGGAGACAAAATTGAAGGAAAAAGAAGACGCACTGGCTAGAATTGAAATTGAAACCCTTCAAAAACAGAAGAAAGTTAAAGTTAAAAAACCAAAACCAGAATTTCCTGTGTATATGCCTTTAGAAAATACGTATATTCAGTCTTATGATCATGGAACTTCTATTGAAGAAATTGAGGAGCAAATGGATGACTGGCTGGAAAACAGGAAAAGAACACAGAAAAGACAGGCACCTGAATGGACAGAAGAGGACCTCAGTCAACTGACAAGAAGTATGGTTAAGTTCCCAGGAGGGACTCCAGGTCGATGGGACAAGATTGCCCATGAATTGGGTCGATCTGTGACAGAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGACAAGATTGCCCATGA
59.3
GCAAAGCCAGCTCAGCATTG
60.74
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGACAAGATTGCCCATGA
59.3
AGCAAAGCCAGCTCAGCATT
60.9
141
PCR template sequence:
GGACCTCAGTCAACTGACAAGAAGTATGGTTAAGTTCCCAGGAGGGACTCCAGGTCGATGGGACAAGATTGCCCATGAATTGGGTCGATCTGTGACAGATGTATGATGATGTTCTGATCAATGGACTTCCAGATTGGCGACAGCCTGTATTCTACTACAGGCGAGTGAGAAAAATGAGCAATGCTGAGCTGGCTTTGCTC
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-9-5p(1), mmu-miR-335-5p(1), mmu-miR-383-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATCTGTGACAGATGTATGATGATGTT
siRNA sets
ATCATCATACATCTGTCAC, CATCATACATCTGTCACAG, AACATCATCATACATCTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDNAJC1_733_ORF_1
1.0376
0.087003373
0.909859216
735
ORF sequence:
ATGTATGATGATGTTCTGATCAATGGACTTCCAGATTGGCGACAGCCTGTATTCTACTACAGGCGAGTGAGAAAAATGAGCAATGCTGAGCTGGCTTTGCTCTTGTTCATTATTCTCACAGTGGGTCACTATGCTGTGGTTTGGTCCATCTACCTGGAAAAGCAACTGGATGAACTGCTTGGTAGAAAAAAGAGAGAAAGGAAGAAGAAGACAGGAAGCAAGAGTGTGGACGCAGCAAAACTTGGTGCTTCTGAAAAGAACGAAAGATTGCTTATAAAACCACAATGGCATGATTTGCTTCCATGCAAACTGGGGATTTGGTTTTGCCTTACACTAAAAGCATTGCCTCATCTAATCCAGGATGCTGGGCAGTTTTATGCAAAATATAAGGAGACAAAATTGAAGGAAAAAGAAGACGCACTGGCTAGAATTGAAATTGAAACCCTTCAAAAACAGAAGAAAGTTAAAGTTAAAAAACCAAAACCAGAATTTCCTGTGTATATGCCTTTAGAAAATACGTATATTCAGTCTTATGATCATGGAACTTCTATTGAAGAAATTGAGGAGCAAATGGATGACTGGCTGGAAAACAGGAAAAGAACACAGAAAAGACAGGCACCTGAATGGACAGAAGAGGACCTCAGTCAACTGACAAGAAGTATGGTTAAGTTCCCAGGAGGGACTCCAGGTCGATGGGACAAGATTGCCCATGAATTGGGTCGATCTGTGACAGAT
Peptide sequence:
MYDDVLINGLPDWRQPVFYYRRVRKMSNAELALLLFIILTVGHYAVVWSIYLEKQLDELLGRKKRERKKKTGSKSVDAAKLGASEKNERLLIKPQWHDLLPCKLGIWFCLTLKALPHLIQDAGQFYAKYKETKLKEKEDALARIEIETLQKQKKVKVKKPKPEFPVYMPLENTYIQSYDHGTSIEEIEEQMDDWLENRKRTQKRQAPEWTEEDLSQLTRSMVKFPGGTPGRWDKIAHELGRSVTD
IRESfinder result
IRESfinder score
0.557640928
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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