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mmu_circMap3k13_557
Basic information of circular RNA
PanCircBase ID:
mmu_circMap3k13_557
mm39_Chr. Position ID:
chr16|21710633|21711190|+
Gene name:
Map3k13
Transcript:
ENSMUST00000231988.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
1
Exon/intron indexes:
3
Exon/intron offsets:
0
Genomic length:
557
Exon/intron sizes in nt:
557
Flanking exon/introns:
chr16:21614725-21710633|chr16:21711190-21717238
Splice length:
557
Other database IDs:
circAtlas: mmu-Map3k13_0001
circBase: hsa_circ_0123036, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_117977
Human Ortholog IDs:
Mature spliced Sequence:
GTTTTGGAGTCCTCTCTTGCATCAAACCTCTGTTGCTGCAATCTTCTGACTGTCATCTCAGGACCTGGGTCACCCTCATGGCACAATGGCCAACCCTCAGGAGCACCTGAGCTGCTCCTCTTTGCCACACTTGCCCTTGACTGAGAACAAAACCTCTGGTGGACGAAATGAGCTTGCAGCTATGGGGAACCACCCTTCACCCAAGCTCCCTGAGGACCCTCAGGAGAGGGGGGCTATACAGTCAGAGCTGATGGAGATCACAGGCAGCCCGATCTCCACAACAGTGTTGACCAGTGTAAGCGAGGATTCTAGGGGCCAGTTTGAGAACAGTGTTCTTCAGCTAAGGGAACAGGATGAGTCAGAGATGACCCTGTCTCTGGGGAACAGCAACACTGTGGATGGAGAGAACACGAACGGACCAGAAGACATCAAGATTCAGTTCAGCAGGTCAGGCAGCGGCAGCGGCGGGTTTCTCGAAGGACTGTTTGGATGTCTCAGGCCCGTGTGGAATATCATTGGGAAGGCATATTCCACTGATTACAAGCTGCAGCAGCAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTTGGATGTCTCAGGCCC
59.96
ACCCAGGTCCTGAGATGACA
59.88
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTTGGATGTCTCAGGCCC
59.96
CCATTGTGCCATGAGGGTGA
60.32
164
PCR template sequence:
GGCAGCGGCGGGTTTCTCGAAGGACTGTTTGGATGTCTCAGGCCCGTGTGGAATATCATTGGGAAGGCATATTCCACTGATTACAAGCTGCAGCAGCAAGGTTTTGGAGTCCTCTCTTGCATCAAACCTCTGTTGCTGCAATCTTCTGACTGTCATCTCAGGACCTGGGTCACCCTCATGGCACAATGGCCAACCCTCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-141-3p(2), mmu-miR-200a-3p(1), mmu-miR-136-5p(1), mmu-miR-370-3p(1), mmu-miR-29b-2-5p(1), mmu-miR-207(1), mmu-miR-300-3p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCAGCAGCAAGGTTTTGGAGTCCT
siRNA sets
GACTCCAAAACCTTGCTGC, ACTCCAAAACCTTGCTGCT, AGGACTCCAAAACCTTGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMAP3K13_557_ORF_1
0.8948
0.203812233
0.806596861
582
ORF sequence:
ATGGCCAACCCTCAGGAGCACCTGAGCTGCTCCTCTTTGCCACACTTGCCCTTGACTGAGAACAAAACCTCTGGTGGACGAAATGAGCTTGCAGCTATGGGGAACCACCCTTCACCCAAGCTCCCTGAGGACCCTCAGGAGAGGGGGGCTATACAGTCAGAGCTGATGGAGATCACAGGCAGCCCGATCTCCACAACAGTGTTGACCAGTGTAAGCGAGGATTCTAGGGGCCAGTTTGAGAACAGTGTTCTTCAGCTAAGGGAACAGGATGAGTCAGAGATGACCCTGTCTCTGGGGAACAGCAACACTGTGGATGGAGAGAACACGAACGGACCAGAAGACATCAAGATTCAGTTCAGCAGGTCAGGCAGCGGCAGCGGCGGGTTTCTCGAAGGACTGTTTGGATGTCTCAGGCCCGTGTGGAATATCATTGGGAAGGCATATTCCACTGATTACAAGCTGCAGCAGCAAGGTTTTGGAGTCCTCTCTTGCATCAAACCTCTGTTGCTGCAATCTTCTGACTGTCATCTCAGGACCTGGGTCACCCTCATGGCACAATGGCCAACCCTCAGGAGCACCTGA
Peptide sequence:
MANPQEHLSCSSLPHLPLTENKTSGGRNELAAMGNHPSPKLPEDPQERGAIQSELMEITGSPISTTVLTSVSEDSRGQFENSVLQLREQDESEMTLSLGNSNTVDGENTNGPEDIKIQFSRSGSGSGGFLEGLFGCLRPVWNIIGKAYSTDYKLQQQGFGVLSCIKPLLLQSSDCHLRTWVTLMAQWPTLRST
IRESfinder result
IRESfinder score
0.490237257
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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