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mmu_circMtr_360
Basic information of circular RNA
PanCircBase ID:
mmu_circMtr_360
mm39_Chr. Position ID:
chr13|12262204|12265577|-
Gene name:
Mtr
Transcript:
ENSMUST00000099856.6
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,574,2526,3283
Genomic length:
3373
Exon/intron sizes in nt:
107,93,70,90
Flanking exon/introns:
chr13:12259503-12262204|chr13:12265577-12268649
Splice length:
360
Other database IDs:
circAtlas: mmu-Mtr_0013
circAtlas: hsa-MTR_0032
Human Ortholog IDs:
Mature spliced Sequence:
GAATACTTGCTGGCTGGAGCAGATATCATCGAAACAAACACTTTCAGCAGTACTAGTATCGCCCAGGCTGACTATGGCCTTGAACACTTGGCCTACCGGATGAACAAGTGCTCTGCAGATGTGGCCAGAAAAGCCGCTGAGGAGATAACTCTGCAGACAGGAGTCAAGAGGTTTGTGGCTGGAGCTCTGGGTCCGACTAATAAGACACTTTCTGTCTCCCCATCTGTGGAAAGGCCAGATTATAGGAACATCACATTTGATGAGCTTGTTGACGCATACCAGGAGCAGGCCAAGGGACTGCTGGATGGCAGGGTCGACATCTTACTCATTGAAACAATTTTTGATACAGCTAATGCCAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATGGCAGGGTCGACATCTT
59.82
CCGGTAGGCCAAGTGTTCAA
60.25
156
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGCAGGGTCGACATCTTAC
59.46
CCGGTAGGCCAAGTGTTCAA
60.25
154
PCR template sequence:
TGAGCTTGTTGACGCATACCAGGAGCAGGCCAAGGGACTGCTGGATGGCAGGGTCGACATCTTACTCATTGAAACAATTTTTGATACAGCTAATGCCAAAGAATACTTGCTGGCTGGAGCAGATATCATCGAAACAAACACTTTCAGCAGTACTAGTATCGCCCAGGCTGACTATGGCCTTGAACACTTGGCCTACCGGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-339-5p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
AGCTAATGCCAAAGAATACTTGCTGG
siRNA sets
AGTATTCTTTGGCATTAGC, AAGTATTCTTTGGCATTAG, GTATTCTTTGGCATTAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMTR_360_ORF_1
1.215
0.313886789
0.940711284
621
ORF sequence:
ATGAACAAGTGCTCTGCAGATGTGGCCAGAAAAGCCGCTGAGGAGATAACTCTGCAGACAGGAGTCAAGAGGTTTGTGGCTGGAGCTCTGGGTCCGACTAATAAGACACTTTCTGTCTCCCCATCTGTGGAAAGGCCAGATTATAGGAACATCACATTTGATGAGCTTGTTGACGCATACCAGGAGCAGGCCAAGGGACTGCTGGATGGCAGGGTCGACATCTTACTCATTGAAACAATTTTTGATACAGCTAATGCCAAAGAATACTTGCTGGCTGGAGCAGATATCATCGAAACAAACACTTTCAGCAGTACTAGTATCGCCCAGGCTGACTATGGCCTTGAACACTTGGCCTACCGGATGAACAAGTGCTCTGCAGATGTGGCCAGAAAAGCCGCTGAGGAGATAACTCTGCAGACAGGAGTCAAGAGGTTTGTGGCTGGAGCTCTGGGTCCGACTAATAAGACACTTTCTGTCTCCCCATCTGTGGAAAGGCCAGATTATAGGAACATCACATTTGATGAGCTTGTTGACGCATACCAGGAGCAGGCCAAGGGACTGCTGGATGGCAGGGTCGACATCTTACTCATTGAAACAATTTTTGATACAGCTAATGCCAAA
Peptide sequence:
MNKCSADVARKAAEEITLQTGVKRFVAGALGPTNKTLSVSPSVERPDYRNITFDELVDAYQEQAKGLLDGRVDILLIETIFDTANAKEYLLAGADIIETNTFSSTSIAQADYGLEHLAYRMNKCSADVARKAAEEITLQTGVKRFVAGALGPTNKTLSVSPSVERPDYRNITFDELVDAYQEQAKGLLDGRVDILLIETIFDTANAK
IRESfinder result
IRESfinder score
0.451181206
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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