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mmu_circMkln1_605
Basic information of circular RNA
PanCircBase ID:
mmu_circMkln1_605
mm39_Chr. Position ID:
chr6|31395865|31410066|+
Gene name:
Mkln1
Transcript:
ENSMUST00000026699.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,7783,9206,12209,14008
Genomic length:
14201
Exon/intron sizes in nt:
70,143,89,110,193
Flanking exon/introns:
chr6:31375889-31395865|chr6:31410066-31426430
Splice length:
605
Other database IDs:
circBase: mmu_circ_0001457, CIRCpedia: MMU_CIRCpedia_16125, circAtlas: mmu-Mkln1_0012
circBase: hsa_circ_0001746, circAtlas: hsa-MKLN1_0012, CIRCpedia: HSA_CIRCpedia_56719
Human Ortholog IDs:
Mature spliced Sequence:
GAACATTTTAGTGGATAAACCAAATGATCAGTCTTCCAGATGGTCTTCAGAGAGCAACTATCCTCCCCAATACTTGATTCTGAAGCTTGAAAGGCCTGCTATCGTTCAGAATATTACATTTGGAAAATATGAGAAAACTCATGTCTGCAATTTGAAGAAATTCAAAGTTTTTGGTGGAATGAATGAAGAAAATATGACAGAGCTGTTGTCCAGTGGCCTGAAGAATGATTATAACAAAGAGACATTTACCTTGAAACATAAAATTGATGAACAGATGTTCCCTTGTCGATTCATTAAAATTGTTCCACTTTTGTCCTGGGGGCCCAGCTTTAACTTTAGCATCTGGTATGTTGAACTTAGTGGCATTGATGATCCTGATATCGTGCAGCCCTGTCTGAACTGGTACAGCAAGTACCGTGAACAGGAAGCCATTCGCCTTTGCCTAAAACACTTCAGACAACATAACTATACAGAGGCTTTTGAATCCCTGCAGAAGAAAACCAAGATTGCACTGGAACATCCAATGTTGACAGATATGCATGACAAATTGGTGTTAAAGGGTGACTTTGATGCTTGCGAGGAGTTGATTGAAAAAGCTGTAAATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGTGACTTTGATGCTTGCG
60.11
AGCAGGCCTTTCAAGCTTCA
60.18
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGTGACTTTGATGCTTGCG
60.11
GCAGGCCTTTCAAGCTTCAG
59.76
146
PCR template sequence:
ATTGCACTGGAACATCCAATGTTGACAGATATGCATGACAAATTGGTGTTAAAGGGTGACTTTGATGCTTGCGAGGAGTTGATTGAAAAAGCTGTAAATGGAACATTTTAGTGGATAAACCAAATGATCAGTCTTCCAGATGGTCTTCAGAGAGCAACTATCCTCCCCAATACTTGATTCTGAAGCTTGAAAGGCCTGCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-135a-5p(1), mmu-miR-26a-5p(1), mmu-miR-130a-3p(1), mmu-miR-7a-5p(1), mmu-miR-320-3p(1), mmu-miR-26b-5p(1), mmu-miR-301b-3p(1), mmu-miR-541-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAGCTGTAAATGGAACATTTTAGTG
siRNA sets
AAATGTTCCATTTACAGCT, AATGTTCCATTTACAGCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMKLN1_605_ORF_1
0.8674
0.15320818
0.532155729
438
ORF sequence:
ATGAATGAAGAAAATATGACAGAGCTGTTGTCCAGTGGCCTGAAGAATGATTATAACAAAGAGACATTTACCTTGAAACATAAAATTGATGAACAGATGTTCCCTTGTCGATTCATTAAAATTGTTCCACTTTTGTCCTGGGGGCCCAGCTTTAACTTTAGCATCTGGTATGTTGAACTTAGTGGCATTGATGATCCTGATATCGTGCAGCCCTGTCTGAACTGGTACAGCAAGTACCGTGAACAGGAAGCCATTCGCCTTTGCCTAAAACACTTCAGACAACATAACTATACAGAGGCTTTTGAATCCCTGCAGAAGAAAACCAAGATTGCACTGGAACATCCAATGTTGACAGATATGCATGACAAATTGGTGTTAAAGGGTGACTTTGATGCTTGCGAGGAGTTGATTGAAAAAGCTGTAAATGGAACATTTTAG
Peptide sequence:
MNEENMTELLSSGLKNDYNKETFTLKHKIDEQMFPCRFIKIVPLLSWGPSFNFSIWYVELSGIDDPDIVQPCLNWYSKYREQEAIRLCLKHFRQHNYTEAFESLQKKTKIALEHPMLTDMHDKLVLKGDFDACEELIEKAVNGTF
IRESfinder result
IRESfinder score
0.762410966
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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