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mmu_circDennd1b_360
Basic information of circular RNA
PanCircBase ID:
mmu_circDennd1b_360
mm39_Chr. Position ID:
chr1|138990598|139018293|+
Gene name:
Dennd1b
Transcript:
ENSMUST00000168527.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,10,11,12
Exon/intron offsets:
0,18312,23022,27593
Genomic length:
27695
Exon/intron sizes in nt:
11,11,01,46,102
Flanking exon/introns:
chr1:138988066-138990598|chr1:139018293-139029705
Splice length:
360
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGAAACCTGACCGAGTACTTTGTTGCCGTGGATGTCAACAACATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCAAATTAAGCACTTTAACTGCCTGTCTCCATGGATCGGCTGCGCTACTCTACCCGATGTACTGGCAACACATATATATCCCCGTGCTTCCTCCACACCTGCTGGACTACTGCTGTGCCCCAATGCCATACCTGATTGGAATACACTCCAGTCTCATAGAGAGAGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCATTGGAAGATGTGGTTGTGT
58.17
CGTACAGTCGCAGCATGTTG
59.91
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCATTGGAAGATGTGGTTGTGT
58.17
ACAGTCGCAGCATGTTGTTG
59.69
142
PCR template sequence:
AGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTGAGAAACCTGACCGAGTACTTTGTTGCCGTGGATGTCAACAACATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
11
Interacting miRNAs (#binding sites)
mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-122-5p(1), mmu-miR-106b-5p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-297a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GCCCAGTGATGTGAGAAACCTGACCG
siRNA sets
GTTTCTCACATCACTGGGC, AGGTTTCTCACATCACTGG, TCAGGTTTCTCACATCACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDENND1B_360_ORF_1
0.9378
0.161098747
0.884459403
678
ORF sequence:
ATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCAAATTAAGCACTTTAACTGCCTGTCTCCATGGATCGGCTGCGCTACTCTACCCGATGTACTGGCAACACATATATATCCCCGTGCTTCCTCCACACCTGCTGGACTACTGCTGTGCCCCAATGCCATACCTGATTGGAATACACTCCAGTCTCATAGAGAGAGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTGAGAAACCTGACCGAGTACTTTGTTGCCGTGGATGTCAACAACATGCTGCGACTGTACGCCAGCATGCTGCATGAGAGGCGCATCATTATTACCTCGAGCAAATTAAGCACTTTAACTGCCTGTCTCCATGGATCGGCTGCGCTACTCTACCCGATGTACTGGCAACACATATATATCCCCGTGCTTCCTCCACACCTGCTGGACTACTGCTGTGCCCCAATGCCATACCTGATTGGAATACACTCCAGTCTCATAGAGAGAGTGAAAAATAAATCATTGGAAGATGTGGTTGTGTTAAATGTTGACACAAACACGTTAGAATCACCATTTAATGACTTGAGCAGCCTGCCCAGTGATGTG
Peptide sequence:
MLRLYASMLHERRIIITSSKLSTLTACLHGSAALLYPMYWQHIYIPVLPPHLLDYCCAPMPYLIGIHSSLIERVKNKSLEDVVVLNVDTNTLESPFNDLSSLPSDVRNLTEYFVAVDVNNMLRLYASMLHERRIIITSSKLSTLTACLHGSAALLYPMYWQHIYIPVLPPHLLDYCCAPMPYLIGIHSSLIERVKNKSLEDVVVLNVDTNTLESPFNDLSSLPSDV
IRESfinder result
IRESfinder score
0.573753118
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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