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mmu_circMap4k3_638
Basic information of circular RNA
PanCircBase ID:
mmu_circMap4k3_638
mm39_Chr. Position ID:
chr17|80913388|80925776|-
Gene name:
Map4k3
Transcript:
ENSMUST00000112389.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
25,24,23,22,21,20,19,18
Exon/intron offsets:
0,3792,6071,7508,7955,9057,10526,12334
Genomic length:
12388
Exon/intron sizes in nt:
61,80,85,42,113,160,43,54
Flanking exon/introns:
chr17:80913313-80913388|chr17:80925776-80925985
Splice length:
638
Other database IDs:
circAtlas: mmu-Map4k3_0061
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
AGGACATGTGGCACACTTAGAAGATGACGAAGGCGACGATGACGACTCTAAGCATTCAACCATGAAAGCAAAAGTCCCGCCTCCTCTGCCACCAAAGCCTAAATCCATCTTCATACCACAGGATACACATTCTGCTGAGGACGGTAATCAAGGAACAATCAAGAGATGTCCCTCATCAGGGAGCCCGGCAAAGCCATCCCACGTTCCACCTAGACCACCTCCGCCCAGGTTACCGCCACAGAAGCCTGCTGTTTTAGGAAATGGAGTGAACTCCTTCCAGCTAAATGGTGAGCGAGACGGATCATTATATCAGCAGCAGAGTGAGCAAAGAGGCACAAACCTTTCAAGAAAGGAGAAGAAGGACGTCCCGAAACCAATTAGTAATGGTCTTCCCCCAACACCTAAAGTGCATATGGGAGCGTGTTTTTCAAAGGTTTTTAATGGATGTCCCTTGAAAATCCACTGTGCCACATCCTGGATAAACCCAGACACGAGAGACCAGTACTTGATATTTGGCGCTGAAGAGGGCATTTATACCCTTAATCTCAATGAACTTCATGAAACATCAATGGAACAGCTGTTCCCCCGCAGGTGTACGTGGCTGTATGTGATGAACAATTGCCTGCTGTCAGTCTCGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGTGTACGTGGCTGTAT
60.11
CTTTGGTGGCAGAGGAGGC
60.68
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGGTGTACGTGGCTGTAT
60.11
GCTTTGGTGGCAGAGGAGG
60.68
149
PCR template sequence:
CTTAATCTCAATGAACTTCATGAAACATCAATGGAACAGCTGTTCCCCCGCAGGTGTACGTGGCTGTATGTGATGAACAATTGCCTGCTGTCAGTCTCGGAGGACATGTGGCACACTTAGAAGATGACGAAGGCGACGATGACGACTCTAAGCATTCAACCATGAAAGCAAAAGTCCCGCCTCCTCTGCCACCAAAGCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-298-5p(1), mmu-miR-7a-5p(1), mmu-miR-214-3p(1), mmu-miR-136-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGTCAGTCTCGGAGGACATGTGGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMAP4K3_638_ORF_1
0.6332
0.034485243
0.58751593
597
ORF sequence:
ATGAAAGCAAAAGTCCCGCCTCCTCTGCCACCAAAGCCTAAATCCATCTTCATACCACAGGATACACATTCTGCTGAGGACGGTAATCAAGGAACAATCAAGAGATGTCCCTCATCAGGGAGCCCGGCAAAGCCATCCCACGTTCCACCTAGACCACCTCCGCCCAGGTTACCGCCACAGAAGCCTGCTGTTTTAGGAAATGGAGTGAACTCCTTCCAGCTAAATGGTGAGCGAGACGGATCATTATATCAGCAGCAGAGTGAGCAAAGAGGCACAAACCTTTCAAGAAAGGAGAAGAAGGACGTCCCGAAACCAATTAGTAATGGTCTTCCCCCAACACCTAAAGTGCATATGGGAGCGTGTTTTTCAAAGGTTTTTAATGGATGTCCCTTGAAAATCCACTGTGCCACATCCTGGATAAACCCAGACACGAGAGACCAGTACTTGATATTTGGCGCTGAAGAGGGCATTTATACCCTTAATCTCAATGAACTTCATGAAACATCAATGGAACAGCTGTTCCCCCGCAGGTGTACGTGGCTGTATGTGATGAACAATTGCCTGCTGTCAGTCTCGGAGGACATGTGGCACACTTAG
Peptide sequence:
MKAKVPPPLPPKPKSIFIPQDTHSAEDGNQGTIKRCPSSGSPAKPSHVPPRPPPPRLPPQKPAVLGNGVNSFQLNGERDGSLYQQQSEQRGTNLSRKEKKDVPKPISNGLPPTPKVHMGACFSKVFNGCPLKIHCATSWINPDTRDQYLIFGAEEGIYTLNLNELHETSMEQLFPRRCTWLYVMNNCLLSVSEDMWHT
IRESfinder result
IRESfinder score
0.406178657
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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