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mmu_circRnf13_333
Basic information of circular RNA
PanCircBase ID:
mmu_circRnf13_333
mm39_Chr. Position ID:
chr3|57671677|57686929|+
Gene name:
Rnf13
Transcript:
ENSMUST00000041826.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
2,3,4
Exon/intron offsets:
0,4783,15126
Genomic length:
15252
Exon/intron sizes in nt:
126,81,126
Flanking exon/introns:
chr3:57643621-57671677|chr3:57686929-57703618
Splice length:
333
Other database IDs:
CIRCpedia: MMU_CIRCpedia_215760, circAtlas: mmu-Rnf13_0014
circBase: hsa_circ_0067716, circAtlas: hsa-RNF13_0017, CIRCpedia: HSA_CIRCpedia_43986
Human Ortholog IDs:
Mature spliced Sequence:
GTGATTCACAAGATGCTGCTCTCCATTGGGATGCTCATGCTGTCCGCCACACAGGTCTACACCATCTTGACTGTGCAGCTCTTTGCATTCCTAAACCTGCTGCCTGTAGAAGCAGACATTTTAGCATATAATTTTGAAAATGCATCTCAGACATTTGAGGACCTTCCAGCAAGATTTGGTTATAGACTACCAGCTGAAGGCTTAAAGGGTTTTCTGATTAACTCAAAACCAGAGAATGCGTGTGAACCCATAGTGCCTCCACCACTGAAAGACAATTCTTCCGGCACGTTCATCGTGCTGATTAGAAGACTTGATTGCAATTTTGATATAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGTGAACCCATAGTGCCT
60.04
ATGGTGTAGACCTGTGTGGC
59.68
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGTGTGAACCCATAGTGCCT
60.04
GGACAGCATGAGCATCCCAA
60.39
140
PCR template sequence:
GAATGCGTGTGAACCCATAGTGCCTCCACCACTGAAAGACAATTCTTCCGGCACGTTCATCGTGCTGATTAGAAGACTTGATTGCAATTTTGATATAAAGGTGATTCACAAGATGCTGCTCTCCATTGGGATGCTCATGCTGTCCGCCACACAGGTCTACACCATCTTGACTGTGCAGCTCTTTGCATTCCTAAACCTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-206-3p(1), mmu-miR-15b-5p(1), mmu-miR-214-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTGATATAAAGGTGATTCACAAGA
siRNA sets
AATCACCTTTATATCAAAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRNF13_333_ORF_1
0.9591
0.13219356
0.856295644
654
ORF sequence:
ATGCTGCTCTCCATTGGGATGCTCATGCTGTCCGCCACACAGGTCTACACCATCTTGACTGTGCAGCTCTTTGCATTCCTAAACCTGCTGCCTGTAGAAGCAGACATTTTAGCATATAATTTTGAAAATGCATCTCAGACATTTGAGGACCTTCCAGCAAGATTTGGTTATAGACTACCAGCTGAAGGCTTAAAGGGTTTTCTGATTAACTCAAAACCAGAGAATGCGTGTGAACCCATAGTGCCTCCACCACTGAAAGACAATTCTTCCGGCACGTTCATCGTGCTGATTAGAAGACTTGATTGCAATTTTGATATAAAGGTGATTCACAAGATGCTGCTCTCCATTGGGATGCTCATGCTGTCCGCCACACAGGTCTACACCATCTTGACTGTGCAGCTCTTTGCATTCCTAAACCTGCTGCCTGTAGAAGCAGACATTTTAGCATATAATTTTGAAAATGCATCTCAGACATTTGAGGACCTTCCAGCAAGATTTGGTTATAGACTACCAGCTGAAGGCTTAAAGGGTTTTCTGATTAACTCAAAACCAGAGAATGCGTGTGAACCCATAGTGCCTCCACCACTGAAAGACAATTCTTCCGGCACGTTCATCGTGCTGATTAGAAGACTTGATTGCAATTTTGATATAAAG
Peptide sequence:
MLLSIGMLMLSATQVYTILTVQLFAFLNLLPVEADILAYNFENASQTFEDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPLKDNSSGTFIVLIRRLDCNFDIKVIHKMLLSIGMLMLSATQVYTILTVQLFAFLNLLPVEADILAYNFENASQTFEDLPARFGYRLPAEGLKGFLINSKPENACEPIVPPPLKDNSSGTFIVLIRRLDCNFDIK
IRESfinder result
IRESfinder score
0.777398026
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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